Peter Butler is providing a guided tour of the facially disfigured. "Here we've got a guy who had his nose taken off. He came across someone wielding a samurai sword - not a good idea on a Saturday night." There's just a hole where a nose should be - awful. "This is somebody who has three-quarter face burns. This is the end result of 40 to 50 operations, skin graft after skin graft after skin graft: it doesn't look great." The patient looks little better after the operations than before.

He scrolls forward on his laptop, and each picture is more devastating than the previous one. "Here is a young girl after her house caught fire. No hair, her eyes dragged down, sausage lips. That's the end of plastic surgery, and it's horrendous. This girl was eight, and she's 12 now." This girl is too young to be a candidate for a face transplant, so he scrolls again, past an Indian girl whose face was ripped off after her hair had been caught in a threshing machine. She'd be perfect, if she wasn't also so young.

He stops at a woman who was involved in a road traffic accident caused by a drunk driver. There is a photograph taken on the day of her accident. She is beautiful, smiley, with long, black hair. And there is a photograph taken after: she has no nose, no ears, no hair, no left eyelid, very little sight and no fingers. Jacqueline Saburido, who became a poster girl for anti-drink-driving campaigns in Texas, is a candidate for Butler's first complete facial transplant.

Butler has been planning this for 15 years. When the plastic surgeon first started thinking about it, he probably expected to carry out the world's first facial transplant. Over the past couple of years, Butler has been overtaken and now there have already been three successful transplants by three different teams - two in France and one in China. But these have been partial transplants - taking a triangle of face including lips and nose, and transferring them from donor to recipient. Butler is planning to transplant the whole face.

Not surprisingly, he has met with resistance. After all, this is the stuff of gothic horror, grave robbers and Victorian freaks shows. Butler has been battling against superstition and prejudice for the past decade. Perhaps surprisingly, most of the resistance has come from a conservative medical profession convinced that face transplants could do more harm than good. There are so many issues to consider: will the face transplant take? Will the recipients feel like themselves or a stranger? Will they have to live the rest of their life on immunosuppressant drugs to prevent rejection? Will the face be fully functioning? And, perhaps most important, will the recipients be any happier?

In October 2006, a year after the first operation was carried out successfully in Amiens, France, Butler was given permission by the Royal Free Hospital's ethics committee to go ahead. He thought it would probably take a year until he was ready for the first operation. Today, he says he's probably still a year away and that progress never happens quite as fast as you hope it will.

Butler works on the ninth floor of the Royal Free Hospital in Hampstead, north London, where he is clinical director for surgery and leads the UK's face transplant team. On his office wall is a framed photograph of the cruelly disfigured John Merrick, better known as the Elephant Man. The photograph is signed: "Dear Freddie, a thousand thanks for the whitewash. Love and best wishes, John." Freddie is thought to be his physician. There is something very moving about the photograph - Merrick is standing in his newly painted attic flat, posing like a model, at ease with himself and his appearance.

Butler is working with those who are not so at ease with themselves. He is drawing up a long-list of potential patients for the first operation. There are so many boxes a candidate has to tick before he or she will even be considered for a face transplant. Children are excluded for now, as are people with body dysmorphia, drug addicts and those who don't need all their face replaced.

Four hundred thousand people in the UK have a facial disfigurement, and for 250,000 of them it is severe. Research suggests that the suicide rate of the severely disfigured is four times the national average and that 60% suffer from social isolation. "Some of the people we see have a life which they term as an existence," Butler says. "They spend their days inside, go to the local corner store in the evening, don't go to the supermarket because they don't want to be seen, they wear a hood or a veil, they take their weekly provision and go home. They don't answer the door even to the postman. That isn't a life. It really isn't."

Butler is a big, handsome man - a cross between Gordon Brown and Clark Kent before he spins into Superman. He looks a young 45, yet at the same time he seems older than his years.

He grew up in Dublin. His father was dean of dentistry at Trinity College and his mother a pharmacist. Today, after years of flitting between America and the UK and Ireland, he has a creamy, mid-Atlantic accent. At school he was a talented artist and he considered going to art college before opting for medicine. Specialising in plastic surgery seemed to be a way of combining the artistic with the scientific. "As I went through surgery, I found plastic surgery appealed to me because it had a creative element to it, and a narcissistic element. Plastic surgery is the last general speciality. I operate on children to very old adults, and I operate on any region of the body from the toe to the top of the head. I also operate on people when other surgeons or physicians have problems, because they can't get a wound to close or they've taken out a big cancer and they've got a gaping hole."

Butler was 24 when he first considered the possibility of a facial transplant. As a trainee surgeon in Dublin, he came across a young man who had been disfigured by fire. His lips were hanging down, he was dribbling, he had lost his nose and his ears, the skin around the eyes was stretched down so he couldn't look forward. "It was hard for him to leave the house because the injuries were so bad that people couldn't bear to look at him. And I just thought that there had to be something better for a boy like him. I felt that as doctors we had to work to try to give him some kind of future."

He's looking at the heartbreaking pictures of Jacqueline Saburido. It's eight years since her accident (she was trapped in a car when it burst into flames), and she's now 28. She has burns on 60% of her body, most of them third-degree. "As she says of herself: two of her friends died, unfortunately she didn't."

She has already had more than 50 operations and is expected to have another 50. Her face has been rebuilt using thin grafts and thicker flaps of skin and muscle from other parts of the body. The trouble is, the skin doesn't look like face skin, and her face still doesn't look like a face. Go to her website, helpJacqui.com, and you see her somehow managing to smile through her non-face, talking of her mother's bone cancer, the prejudice she recently experienced when she was not allowed into a club because she looked as if she was in "fragile health", and her dreams of a face transplant. "If it had not been for my strength, my determination and my faith in God, that nurtures me everyday, I would have been depressed, crying every day without wanting to get out of my house, or maybe I could have wanted to kill myself after the great humiliation I suffered," she writes. "But that was not the case! Because I know how much I am worth and nothing or nobody is going to stop me from making my rights count and from continuing with the great mission that God has for me and for which he allowed me to stay in this planet."

Although Jacqueline is the right age, has full-facial injuries and a brilliant attitude, even she isn't the ideal patient. "Maybe a bit too severe," Butler mumbles, almost to himself. "She has so much damage that she might be too difficult to do as the first case." She would also have to move to Britain permanently to be monitored after the operation.

The surgery is difficult, but it is not revolutionary. Butler says plastic surgery goes back thousands of years, and shows me an illustration to prove the point - a post-operative man in India that is thought to date back to 2,000BC. His nose had been chopped off, probably for adultery, and has been recreated using flaps of skin from the forehead. Strap it to the place where the nose had been, leave to settle for a few weeks as the skin re-attaches itself, cut and reshape and, voilà, you have a new nose. Even the knives and scalpels from 2,000BC look familiar.

It is everything surrounding the surgery that presents the biggest challenge: finding a face that matches in tone and texture; persuading the family of the deceased to donate it; ensuring the face is removed and transferred rapidly enough to be stitched on to the recipient (four to six hours); making sure the recipient is psychologically adjusted to the idea of living with a new face.

Butler works with a psychologist, Alex Clarke, who is preparing the 31 potential recipients for their transplant. The new face will look like a hybrid of donor and recipient. Butler shows me computerised models in which he has taken on Clarke's face and she has taken his. "You have mainly the cranial facial skeleton coming through, but the skin tone and texture is of the donor. If you match them for skin tone you should get more of the recipient than the donor."

I yelp in surprise, looking at the computer-generated image. It's spooky because he now looks so female. "But this isn't a good example," he says quickly, "because it's female to male. We'd always do male to male or female to female." When he carries out his first transplants, he intends to take the skin and fatty tissue, what he calls the skin envelope, but not the muscle (he will choose a recipient who still has facial muscles). When he shows me a male-on-male transplant, the recipient does look more like his old self than the donor.

A common fear among donor families is that they will see the face of their loved one walking down the street. (Having seen him morphing into Clarke, I understand why.) But the biggest battle they have had to fight is against the "Face/Off scenario". In the 1997 film Face/Off, John Travolta and Nicolas Cage swap faces and transfer personalities in doing so. Butler finds it unbelievable that so many people believed this to be the actuality of face transplantation.

While this might be far-fetched, more subtle psychological issues are understandable, as Isabelle Dinoire, a French woman who received the first facial transplantation, soon found out. The media, especially the British press, lost little time in investigating the background to the Dinoire story. Before long it was discovered that she had been depressed, taken pills, and ended up unconscious. As she lay unconscious, unable to respond to her dog's attentions, it appears that the dog went berserk and mauled her. It later emerged that her new face had come from a donor who had committed suicide.

The French media behaved with restraint, but there were articles in the UK press suggesting that Dinoire did not deserve her new face, that she was in no fit state to give her consent, that she was haunted by the ghost of her donor. The truth appears to be that she experienced a degree of strangeness - an odd taste in her mouth; her chin sprouted a hair for the first time; she found herself telling her daughter "her nose was itching" and then saying, "That's nonsense. It's not my nose. I have a nose that is itching." However, she regarded her donor as her "saviour" and was thankful for her new life.

Bernard Devauchelle, professor at Amiens hospital, led the 50-strong team that operated on her. He says he was fully prepared for the operation and its after-effects, but wholly unprepared for the reaction among the British media. "Maybe we were naive," he says. In France, Dinoire and the donor family were protected by privacy laws. Devauchelle says that every nation's media had a distinctive take on the story. "The American media are more interested in the scientific point of view, the Brazilian media are just interested in the aesthetic aspect, the French media are more interested by the controversy, because some philosophers and surgeons were against the transplant. And some bad journalists in England were just interested in trying to contact the donor family."

He and his team are still in close contact with Dinoire. "In the first year we saw a lot of improvement in terms of function and aesthetics and sensitivity," Devauchelle says. "Little by little we see how she has the possibility of emotion in her face. Now the transplant is perfectly integrated on her face, and she can speak, she can smile and she can translate the emotion. She is totally integrated into society. She has a normal life at home with her two girls, and she hopes to get a job."

Devauchelle and his team have permission to do five more transplants, but like Butler they are not rushing. It is so difficult, he says, to find the perfect recipient. The funny thing is, he says, he had never given face transplantation any thought until they invited Butler to Amiens five years ago to talk about his futuristic vision. "Peter Butler was the first in the world. Unfortunately for him he didn't have any possibility to put his ideas into practice due to the law in Britain, but now he receives authorisation. And Peter came here at the beginning of the year and we had a new discussion with him, and it's good because we swap information. If he needs some help, we can bring this help."

Back at the Royal Free in London, Butler is telling me that every time there was a new story about Dinoire, he'd be phoned up by journalists. "When Isabelle had her face done, the Sunday Times ran a banner headline saying, 'Donor committed suicide', and I said, 'Isn't it great that something good has come out of a tragedy?' " For all that, doesn't he think that when Dinoire discovered that her donor had killed herself, it could have traumatised her? "No, absolutely not. It's hocus pocus and black magic. You're really getting worried about a characteristic of the donor being transplanted with the piece of tissue into the recipient." He laughs. "You guys are supposed to be intelligent."

A few weeks later he was called by a newspaper to comment on the shock-horror story that Dinoire was now smoking. "I said, well, actually, smoking doesn't really interfere with the healing, only early on. She must be getting a lip seal. Isn't that wonderful? You have to be able to make it into a sphincter to be able to suck. But they didn't publish that."

Butler has had more substantive issues to contend with. For years the Royal College of Surgeons has opposed him, arguing that there were long-term risks of patients rejecting the face, leaving them worse than before, and that they would always have to take immuno-supressant drugs.

Well, he says, the world's first three face transplants refute the notion that a new face will be rejected. As for the lifelong drugs regime, "If you roll the risks into one of taking a lifetime of immuno-supressants, it's equivalent to losing 10 years of life, but most patients we talk to with facial disfigurement say, 'I'd rather have 10 years of a more normal life than a lifetime of what I've got.' The key issue is the risk-benefit ratio."

Another genuine problem is finding donors. The idea of donating a face or hand makes people squeamish. He directs me to research showing that if you don't agree to donate a cornea, you are unlikely to agree to a hand or face. Why is that? "They are external organs. That's where the cut-off is. Even Simon Weston [the Falklands war veteran who suffered horrendous burns injuries], who is patron of the charity I have set up, says he wouldn't want to donate a cornea because he feels a bit funny about it."

The face transplant will not be performed on the NHS - at least not initially. Butler thinks it would be too controversial. "You know what you guys would say: 'Why are you allowing him to do this type of thing when Granny needs a hip?'" Each operation would cost £25,000-£30,000 and the immuno-supressive regime would be £5,000-£7,000 a year. Butler has established the charity, Facetrust, to raise money, but has also invested some of his own savings in the project.

How much? "No, no, no, no, I'm not going there," he says. "No way. I can't tell you that. My wife would murder me. She already says, what's this about you spending money?"

Butler is married to Annabel Heseltine, the journalist and daughter of former deputy prime minister, Michael Heseltine. She has said that one of the things that attracted her to him was that he was just about the only man she had taken home who was not in awe of her father. In fact, Butler claims he had hardly heard of him because he had spent so much time in America.

They weren't an obviously matched couple. She was into clubbing, he wasn't. "When I met her, she went to these socially things and I couldn't stand them so I used to avoid them, and she just stopped going." They had their first children, twins, after IVF treatment. Now they have four kids, aged between five and two. Butler says he likes to get home to put them to bed and read them a story, but admits that it doesn't always happen. "She definitely has the dominant role in the parenting."

About 90% of Butler's work is for the NHS, mainly operating on skin cancers and facial disfigurements. The other 10% is private - typically nose and breast surgery. But he says it's too simplistic, and judgmental, to draw a line between cosmetic and reconstructive surgery. When it comes down to it, a face transplant for the most severely disfigured is still a form of cosmetic surgery.

Does he think there will come a point when people opt for a face transplant simply because they are bored with their face and would prefer somebody else's? He laughs. Not a chance, he says. After all, patients will not have fully functioning faces after the operation. "They get 95% return of sensory function and 75% return of motor function. That's why it would never be used as a cosmetic surgical operation because it's not a return of normality. It's a massive improvement for people who start with bad facial injuries but, Jesus, if you're a cosmetic patient, you'd never go there because it's actually going backwards. And then there's all the immuno-supressants you'd have to take."

How does he know that he will have the skills to do the operation? "I've practised on cadavers. I've done 111 facial dissections - taking the faces off and swapping them over." He pauses. "But they still looked like cadavers, so it wasn't that useful." The retrieval takes two to three hours, and the operation itself will last around 12 hours. He's not sure if the process will become commonly used. In a few years, he says, transplantation could be superseded by tissue engineering.

Even between colleagues, facial transplantation is still a contentious area - disagreements rage. The French team claim that full facial transplantation is impossible at the moment. Professor Sylvie Testelin, who was part of Devauchelle's team, says, "The problem with full face is the eyelid; you cannot do a full facial transplant without the possibility that the patient will not be able to see because he cannot open his eye." He'd be blind? "Not blind, but the eye cannot move. So either the lid is up or it is down. But obviously Peter Butler knows that. Even if he speaks of 'full facial transplantation', it cannot include eyelids. Impossible."

Butler concedes that the French team have a point if we are talking about transplanting muscle, but his technique will largely involve transplanting skin and fatty tissue, and re-attaching them to the muscle of the patient. Most of the patients he has assessed have functioning eyelids, and it would just be the eyelid skin that he'd replace.

The French team believe that you also have to transfer muscle to give sufficient mobility to the face, and wonder whether the full face transplant will end up as a glorified skin graft. "Physiologically it's impossible to do a facial transplant only with skin, you have to take muscle - if not, it's only a covering, it's not a mobile face. If you don't have motion in your face, it's not a face, it's a mask," Testelin says.

Butler says his job is to replace what is missing and damaged - why would he replace working muscle when it helps retain facial expression? But he insists that it would not be truthful of him to promise 100% function; that there is bound to be some scarring in the raising and replanting of the skin envelope. He's coming from a different starting point than the French, he says. His patients are so severely disfigured and functionally impaired that they will be thankful for 75% return of motor function - and he stresses this is a conservative estimate. "They say, 'I'll take that, thank you, because they are functioning at 10%, 20%, 30%, so this is improving significantly."

Butler is thinking about the French team's comment that his new face might just be a mask. "This is simply not true; obviously function is hugely important. But interestingly, when we've talked to patients about that, most people would say that I'd rather have a normal-looking mask than what I've got now."

Both teams are hugely respected among medics and scientists. Despite their protestations that this has not been a race, and that they hope to continue working together, the world of surgery, especially innovative surgery, is famously competitive. Does it upset Butler that he didn't get there first? No, he says, the two teams have just done things in a different order. Whereas they found a patient and then got ethical approval, he got ethical approval first and then looked for patients. He feels that's the right way round. Anyway, he could still be the first to perform a full facial transplant.

Surgeons have a reputation for being macho, I say to him. How much of this project is idealism and how much is pure ambition? "I'm not macho at all," he says. "I've always questioned what I've done and asked if I could do it better, even minor surgical processes. First look at the evidence, re-examine it, and use the evidence-based approach, and try to make your patients' lives better. What matters is that you make people fully functioning members of society. So whether I am first or last makes no bloody difference, because I know I've contributed to moving this debate forward in an educated and methodical way, and I think that's more important than the end point in itself." ·

· Peter Butler (Facetrust.org) will give a talk at FACT in Liverpool today at 5.15pm, which will be broadcast as part of Radio 3's Free Thinking season, which begins tomorrow at 8pm