When we had our little girl, we quickly realised that parenthood was all about choices. Until she was old enough to make her own decisions, the burden would fall on my partner and me to make the best choices for our baby girl. When to start weaning, when to move her to sleep in her own room, which nursery to opt for: a minefield of decision-making lay before us, all of which would have an impact on her shiny new existence.

So why didn't we think twice about having her immunised? Our instinct was to accept NHS recommendations, and that's what we blithely did. The "five-in-one" injection (or DtaP/ IPV/HiB) was introduced to Britain in October last year. It is meant to protect children against diphtheria, tetanus, whooping cough, polio and Hib (haemophilus influenza b), and is thought preferable to the jab it replaced because it avoids the need to give a live polio vaccine orally, and eliminates the mercury-based preservative that the other contained. Babies get the new jab at two, three and four months, along with an injection against meningitis C.

The NHS is naturally pro-immunisation, reassuring parents that their babies can easily cope with these jabs. Official literature insists that babies barely react to them, but that if they do, they might be irritable and have a slight temperature for up to 48 hours - that's all. Imagine our terror, then, when our precious bundle was still unwell, and altered, six days after her second jab. She was ill for seven days in total - and no one, it seemed, could tell us why.

Health visitors suggested she had a concurrent cold. The practice nurse echoed the cheering information on the NHS website that it is thought that babies could handle 10,000 vaccines at once. All the books and leaflets that we had accumulated insisted that babies suffer for two days at most.

So why did our baby continue to have a high temperature? Why was she listless and pale? Why less interactive? Why did she have that odd glassy stare and seem completely different to the way she was before we apparently poisoned her?

And why, when I began asking around, did I find half a dozen other mothers whose babies were also ill for about a week - in some cases mildly, but in others with symptoms worse than ours, including severe vomiting and diarrhoea?

Though most people now accept that the suggested link between the MMR and autism does not exist, this was inevitably what we thought of. Cool logic can never entirely eradicate the feeling that it's unnatural to inject serious diseases into tiny babies, and now those worries rose to the fore. Had we been playing Russian roulette with the health of our baby?

Our GP used to work as a paediatrician at Guy's and St Thomas's. She is strongly pro-immunisation, having treated children with the diseases that immunisations aim to eliminate. We went to see her, and she told us that she saw about one baby a month showing a reaction to the immunisation, and one every six months with a reaction that could be classified as severe. She felt our daughter's reaction was unusual compared to those normally reported, but there was nothing much she could do other than recommend Calpol.

The whole episode left us upset, worried and confused, and it was only later, while researching this article, that I got to read the patient information leaflet for Pediacel - the immunisation our daughter had received - as issued by the manufacturer Aventis Pasteur. Apparently the symptoms she experienced are "rare", meaning that they are reported in fewer than 1 in 1,000 cases, but more than 1 in 10,000.

Our baby's mysterious symptoms were all there in the leaflet. She suffered what are described in clinical trials as hypotonic-hyporesponsive episodes - but of course we were never offered this leaflet to read before or after our daughter had the jabs. In fact, we were never offered any information pertaining to the more severe side effects of the jabs. Our GP has since said that the practice assumed this information was given to parents by our health visitors - in fact it wasn't - and it is now looking into providing more details to parents to help bridge the gap.

The Department of Health asserts that it "provides a wealth of resources for parents and health professionals, [including] leaflets, fact sheets and websites on all the vaccines used in the routine immunisation programme, and including information on their safety, efficacy and possible side effects", but the truth is that the information it offers is really rather vague. Of course there are plenty of websites critical of immunisation programmes that one could turn to. But you don't feel you can trust them either. They're full of anecdotal evidence from parents convinced that vaccines damaged their kids: they're very emotive, often verging on the hysterical. What they're not is calmly factual and properly balanced.

Once our daughter had recovered, the next question was: should she have the third jab as scheduled? You might think this would be straightforward, but it wasn't. In fact, no one seemed to agree on it. Health visitors thought we should continue as if nothing had happened and said she would probably suffer less with the third jab. Our GP said she was as likely to suffer just as much with the third, but said if we were worried we could always opt to see another GP and pay to have separate injections, or not to have them at all. The practice nurse said in her experience, babies generally suffered less with the final jab, but there was no hard and fast rule except that it was better to finish the course.

Eventually we waited until she was six months old and stronger before subjecting her to the third jab - and she sailed through it. But another local mother, whose baby's reaction was also severe, was told by her GP she must have the third injection on schedule, or the first two were worthless. That's untrue, as it happens - parents can wait until their child is 11 months old before completing the course, without needing to restart the series.

So should we have been warned about the severe, if rare, side effects of the jabs our daughter was given - and how long they might last for? Doctors naturally worry that too much information can put patients at risk if it deters them from taking medications that could benefit them. Interestingly, though, the Pediacel leaflet, when I got to read it, didn't suggest a time-frame within which to expect side effects after the immunisation. The DoH may say that "experience in the use of a similar vaccine in Canada has shown that the most common reactions seen are minor local reactions within 48 hours. We are not aware that this vaccine routinely causes a child to be ill for long periods of time". But the leaflet does not give such limits, and I think I would have found it helpful to know that it can be longer than 48 hours.

It turns out that, since Pediacel was introduced to the UK, there have been 178 reports of adverse reactions sent to the authorities, although more than two million doses of the vaccine have been given here - that's about eight bad reactions per 100,000, less than was the case for the previous jab.

That's good news. But it doesn't really make up for the fact that we met such a sea of ignorance when things went wrong for us. Health visitors and GPs should surely know that side effects can last for up to seven days.

There are those who have a rather cynical take on this. GPs get bonus payments for hitting immunisation targets, and the last thing they want is people being scared off these jabs, as they were scared off MMR. One mother I spoke to speculated that some medical practitioners adhere to the "party line" that ill effects are experienced for only 48 hours because fewer parents would opt for vaccinations if they knew their kids could be ill for a week.

I'm not quite so cynical, but if parenthood is about making choices for our children, the least we can do is make sure that they are informed choices. Next time my child is about to have a jab, I will ask to see the patient information leaflet first. That way, if things go awry, I'll at least have had some idea of what to expect.