In the living room of Dolly Macdonald's house near Stornoway, on the Isle of Lewis, one photograph (among many of her children) reminds her of the son she used to have. 'At that time, when Craig was a year to 18 months old, she says, 'he was progressing normally, then all of a sudden he wasn't. He sort of disappeared, the child who had been living with us just went.'

That was six years ago before Craig, now nine, was diagnosed as autistic. 'Most children at that age would have played quite happily, mixing with other kids,' says his mother, 'but Craig was content to come into a room, empty all the toy boxes and sit in the middle of it all doing nothing - or sometimes he'd sit and rock. Any language he had, he lost. He'd gone from being a normal baby who babbled, to a toddler who sat and did nothing or was totally hyperactive and just wouldn't stop.'

Today, it is a different story. While Dolly keeps an eye on Rachel, her 13-month-old daughter, Craig is at Knock Primary School, a mainstream school on the Eye Peninsula, a 20-minute drive away. 'The school is quite happy with him,' says his mother. 'He's settled, he's reading, he does his maths, he does everything at his own level. There are times when the school will ring and say he's been a bit off-the-wall, or a bit tired, and I can usually connect it to something. If he's been to a party the day before and eaten something he shouldn't have, he gets fidgety, he can't think or concentrate.'

In a post-Jamie's School Dinners world, it's a fashionable stance to take. Like Oliver, Dolly Macdonald passionately believes not only that a child's diet of junk food, sugar, additives and allergens exacerbated her son's behavioural problems but that changing it altered his mental ability and mood. Controversially, some experts even think poor diet may be a factor in autism, ADHD (attention deficit hyperactivity disorder), low IQ and aggression, something of which Mrs Macdonald is convinced.

'I'm not saying his improvement is all about food,' she says, 'because we did a home-based ABA [applied behavioural analysis] programme with him. But without the diet, I don't think we could have done that - he would have been less able to communicate, had he not been on a diet where we took out all the stuff that was mucking up his wee brain.'

In Craig's case, the offending 'stuff' was initially milk and wheat (the usual suspects, casein and gluten, named in scientific studies of autism and to which many autistic children are intolerant). Craig was no exception, says his mother. 'We just thought milk was good for him, but after we removed it from his diet we saw a difference in three days: he was a lot calmer.'

Later, when the Macdonalds excluded monosodium glutamate (MSG, the flavour enhancer found in crisps and snacks) 'Craig seemed better emotionally and physically'. Last summer, in the final stage of Craig 's rehabilitation, nutritional therapists at the Brain Bio Centre in London began to put foods into his diet as well as taking them out: a teaspoon of omega-3 fish oil every day (to boost brain function); oats (a slow-burn carbohydrate and a good source of the amino acid tryptophan, converted to the 'happy hormone' serotonin); fruit and veg high in fibre (to slow absorption of glucose, regulate blood sugar and, according to his nutritional therapist, stabilise mood); the liquid from soaked linseeds (a source of essential omega-6 fats, known to be good chemical building blocks for the brain) mixed with fruit juice to disguise the texture and taste.

Like all children, Craig also had to be discouraged from eating junk food - based on the controversial hypothesis that the fats and chemical additives in them affected his mood. 'He harps on about that advert for Wall's Balls [coated sausage balls that are 17 per cent fat and only 47 per cent pork],' says Dolly, 'so we made our own with mince, herbs and onions and coated them in bread crumbs – and he thought they were brilliant. He'll even eat fish cakes, home-made, of course. I'd hate to think what state he'd be in if he ate things like Turkey Twizzlers [only 34 per cent turkey, an undisclosed amount of fat and no fewer than eight E-additives].'

At the University Laboratory of Physiology in Oxford, one scientist is wondering the same. 'When it comes to foods that affect children's brains, fat - the quantity and type of fat - is the number one theme,' argues Dr Alex Richardson, senior research fellow and co-director of the charity Food and Behaviour (FAB) Research. Not only are the liquid fats essential to brain development (such as omega-3 fatty acids, found in oily fish) lacking in the modern diet, but their industrial alternatives - hydrogenated and trans fats, which are solid at room temperature - are known to make the brain membrane less flexible and fluid, altering the signalling capacity of its cells.

Animal studies have shown that these man-made fats can be incorporated into the brain's physical structure, and there is strong evidence, Dr Richardson believes, that they can alter the profile of its neurotransmitters or chemical messengers.

Patrick Holford, founder of the Brain Bio Centre that treated Craig Macdonald, claims children who consume these fats 'end up with a thicker brain'.

Deftly, Dr Richardson talks me through the other, more traditional bêtes noires of those who believe there are clear links between a junk-food diet and behavioural problems. Sugary drinks, she firmly believes, can alter the mood of children by triggering energy highs and lows and disturbing brain function - a claim backed up by a handful of studies but disputed by the sugar industry.

'Detailed studies have concluded there is no link between sugar and hyperactivity or any other type of "bad behaviour" or learning difficulties,' says a spokesman for the Sugar Bureau (funded by British Sugar and Tate and Lyle). Children may become overexcited on occasions where sugary foods are eaten, such as birthday parties, but this is a consequence of the situation, not their sugar intake.' The same controversy surrounds E-additives, demonised in Maurice Hansson's book (E for Additives) and implicated in a 1990 study of tartrazine and hyperactivity published in the Journal of Nutritional Medicine. A Government-funded trial using a cocktail of additives, conducted by scientists at Southampton University in 2002, found evidence of a link with hyperactivity in children, based on parental observation - again disputed by the food industry and the Government.

'Though this research is in line with previous reports,' says the Food Standards Agency (FSA), 'the evidence is not conclusive and remains an area of scientific uncertainty.' Nevertheless, the FSA has commissioned further research while Bird's Eye bowed to consumer pressure last year and removed all artificial colourings, flavourings and preservatives from its products. They include E621 (MSG), the flavour enhancer eliminated from Craig Macdonald's diet - now replaced with rosemary extract. The company said it was responding to the 'instinctive concern' of consumers rather than any proven risk.

'My view is that I wouldn't touch them,' said Dr Vyvyan Howard, senior toxicologist at Liverpool University, last year, while overseeing a study of the effect of E-numbers on neurones, the cells that carry brain impulses. 'These additives have been tested one at a time but they haven't been tested in combinations as they appear in foodstuffs. We simply do not know what their long-term effects are.' The same is true of fats, Dr Alex Richardson's specialist area. Most commercially baked products (such as crisps, cakes, biscuits, pastries, popcorn and French fries), she says, contain fats that have been through a process called hydrogenation, and many also contain trans fats, acknowledged by the Food Standards Agency and the US Food and Drink Administration to be harmful. 'Trans fats have no known nutritional benefits,' the FSA confirms, 'but they can raise blood cholesterol levels and increase the risk of heart disease.'

Among the most popular trans-fatty fast foods on offer are KFC Colonel's regular crispy strips and fries (4.4g per portion), McDonald's McNuggets and regular fries (3g) and Burger King Whopper and fries (2.3g), according to a recent Which? report. Similarly, high level trans-fatty foods can be found on all supermarket shelves. The current 'safe' recommendation for trans-fat intake in Britain is 4.4g per day for women and 5.6g for men - but scientists in the US, the Netherlands and Denmark (where trans fats have effectively been banned) say the only safe level is zero. Last November, researchers at the Medical University of South Carolina showed that rats with a high trans-fat intake (with hydrogenated fats making up 10 per cent of their diet) could not perform simple memory tasks as well as those on a soy bean oil diet. Some were five times worse at recalling the location of hidden platforms in a water-filled maze - a finding described as 'quite alarming' by Ann-Charlotte Granholm, principal scientist on the MUSC project. What's more, hydrogenated fats - the only ones some children eat - take the place of healthy polyunsaturates, such as omega-3 fatty acids, needed for brain development.

'Your body absorbs trans fats but can't use them,' Dr Richardson claims, 'they are dysfunctional fats. They get stored in membranes but we can't pull them out and turn them into useful substances.' As well as keeping brain membranes fluid and neurotransmitters signalling efficiently, polyunsaturates are the raw materials used for making a 'super-family' of molecules that regulate the immune system, hormones and blood flow. 'The immune system,' Dr Richardson says, 'is a link between body and mind. Tweak the immune system and you can affect mood.' So far, however, research has focused more on the positive role of essential fatty acids than the negative effects of their junk-food counterparts.

'There's a lot of work showing that omega-3 is depleted in depressed patients and might be helpful in the treatment of depression,' Dr Richardson says - and some evidence that children with disorders like ADHD and autism are deficient in omega-3. 'Anyone lacking omega-3 is likely to be prone to low mood and irritability; and impulsivity seems to be coming through. If you think about badly behaved children with their low frustration tolerance, classroom fights and throwing things at the teacher, these are things that seem to improve in some children if you give them enough omega-3.'

It's a tantalising thought, that all those classroom bullies, surly adolescents and hyperactive 10-year-olds could be tamed with a few drops of Eye Q fish oil - and one teachers must love. In the summer term of 2003, some 624 pupils at British schools were excluded for violence towards teachers or students while 16,800 were suspended for assault; every day, 10 are excluded for poor behaviour while 450,000 are absent from class - enough to fill 816 primary and 252 secondary schools. So far, the Government has pumped £342 million into school behaviour improvement programmes. Could all this be prevented by a daily fish oil capsule?

So confident is Dr Alex Richardson of the links between dietary fats and behavioural disorders such as dyslexia, autism, dyspraxia and ADHD, that most of her research has long been focused in this area. By her own admission, however, studies clearly establishing a link between essential fatty acid intake and ADHD in children have been 'few enough' and the results are 'a mixed picture'. Two trials have shown no firm evidence, while two have had positive results. In 2002, Dr Richardson's own research looked at children aged eight to 12 with specific learning difficulties (mainly dyslexia) and some symptoms of ADHD. Those who were given omega-3 and omega-6 (as opposed to olive oil) showed marked improvements in mood, attention span, concentration and short-term memory. A similar study in the US found the same.

The paucity of evidence, Dr Richardson argues, is partly due to a lack of funding for research like hers. She also believes the patchy results may reflect the wrong kind of omega-3 oils being used, 'ones that are rich in DHA (decosahexaenoic acid) instead of EPA (eicosapentaeonic acid), a key building block for the brain. Other experts say the science simply doesn't add up…yet.'

'There is preliminary evidence that omega-3 fish oils work,' says Professor Eric Taylor, a child neuropsychiatrist at King's College, London, 'but it's too early to tell parents to give them to their children. Until there is unequivocal proof of the beneficial effects - or otherwise - of fish oils on struggling children, parents should stick with traditional psychological treatments which are free on the NHS - and work.'

In 2002, however, Dr Richardson went as far as saying that deficiencies in essential fatty acids 'may contribute to both the predisposition and the developmental expression of dyslexia, dyspraxia, ADHD and autism' -; conditions that are dramatically on the increase, with half a million British children now on Ritalin (the main drug treatment for ADHD) and the World Health Organisation predicting a 50 per cent rise in child mental disorders by 2020. Was the shift to a junk-food diet high in hydrogenated fats and low on fish and seafood largely to blame?

'Diet may be one factor,' Dr Richardson says, 'but it will take a lot more trials to prove it. I'd say that things are pointing strongly that way.'

In a hotel in Singapore, nutritionist Patrick Holford is telling me much the same thing. As he nears the end of a worldwide lecture tour promoting his philosophy of 'optimum nutrition', he takes time off to explain the links between diet and the mushrooming trend in child behavioural problems. 'There's absolutely no question that food is a major factor affecting how children perform, feel and think,' he claims. 'If you supplement their diet with vitamins and minerals, you get an improvement in their IQ and concentration.' One reason, he believes, is that essential nutrients have been stripped from the modern diet. 'If you refine something like flour or sugar, you remove 98 per cent of the chromium - which is absolutely essential for controlling blood-sugar levels. Chromium works effectively with insulin to keep your blood sugars even - and the brain, more than any other organ, needs a stable supply of glucose. If it doesn't get it, you will notice dramatic changes in a child's mood.'

It's an argument you might expect from a man who sells multivitamin supplements and uses them heavily at his Brain Bio Centre, but the theory is backed up by independent research. In 2002, a landmark study by Bernard Gesch of Oxford University showed a 35 per cent drop in violent behaviour in prisoners who had minerals and essential fatty acids added to their diet.

Last year, scientists at the University of Southern California found children were more likely to be violent in their teens if they had been deprived of zinc, iron, B vitamins and protein early on. Research has also shown that half of Britain's schoolchildren suffer from zinc deficiency, associated with a high-fat, refined diet lacking not just zinc but iron, protein, calcium, folate and vitamins A and C. As a result, school caterers are given guidelines on where these nutrients are found. Among the effects of zinc deficiency are a reduced ability to metabolise sugar (linked to mood swings) and an impaired sense of taste and smell, making salty, sugary foods more appealing than subtly flavoured fruit and veg - as seen on Jamie's School Dinners. Unfortunately, refusal to try a wide range of fresh and wholefoods deprives children of the very nutrients they need for emotional stability.

So what are today's parents to do? One hope lies in turkey and chicken, regarded as palatable by children. It is a source of tryptophan, an amino acid (or protein fragment) converted by the body into serotonin, the 'happy hormone' that enhances mood. Sources of tryptophan, according to nutritionists, are lean meats, fish, beans and lentils. Complex carbs such as wholegrain pasta, oatcakes and fruit are thought to help the body absorb tryptophan and convert it into serotonin, while the way they are broken down by the body - a steady release of glucose into the blood stream, as opposed to the energy 'rush' of refined carbs (such as sugar or white bread) - are believed by some to moderate mood. Low-GI (Glycaemic Index) foods, including rye bread and basmati rice, also release glucose slowly, while high-GI foods (baguettes, instant white rice) are cited by some as the foods most likely to provoke erratic behaviour.

These and other principles are outlined by nutritionist Amanda Geary, creator of the Mood Food Project, an initiative supported by the mental-health charity Mind. Indeed, something called the Mind Meal (wheat-free pasta with pesto sauce and oil-rich fish, followed by avocado salad and seeds, then fruit and oatcake for dessert) is applauded on the project's website by Nigella Lawson. But how much truth is there in the suggestion that the harsh release of glucose in the bloodstream can influence mood?

'Most of us experience a blood-sugar low,' says Deborah Colson, the nutritional therapist who treated Craig Macdonald at the Brain Bio Centre, 'and the irritability and poor concentration that goes with it. We lose our temper and, as soon as we've had a cup of tea and a biscuit, we feel better. It's the same with children who have eaten sugar-laden cereal for breakfast. By 11 in the morning, their blood sugars will have plummeted.' While blood sugar levels may make the difference between feeling jaded and feeling fine, do they lead to mood swings as some claim? Hyperactive children do consume more sugar than others (but this may be an effect not a cause). In one study of 265 hyperactive children, three-quarters had abnormal glucose tolerance (they could not process sugar properly). In 2002, a questionnaire returned by 800 teachers in south-west England showed pupils were at their most troublesome between morning break and lunch, possibly due to the consumption of sugary drinks. Most scientists say any such link is tenuous. However, three years ago, teachers at Charles Burrell High School, Thetford, Norfolk, banned the sale of fizzy drinks on the grounds that their high sugar content causes disruptive behaviour. Vending machines were removed, drinking water fountains were installed. 'I am absolutely convinced that certain children react disastrously to a high sugar intake,' says Robert Ogden, the assistant head teacher. 'Their concentration disappears, it prevents them from learning, it gives them a sudden energy buzz. A third of the children in our school are on the special needs register, so they have a lot of issues anyway. The big sugar rush and the buzz of energy can mean it's difficult to stay seated, for one thing. We can't say that children don't bring fizzy drinks in or have access to them, but they can't buy them here. We've kept giving them the message that water is a good thing. We allow water in class.'

Since 2002, the soft-drinks ban and other measures (including a positive behaviour management programme) has boosted attendance levels to 91 per cent, up from about 80 per cent; the GCSE pass rate has doubled.…#65279; 'The drinks ban is not the whole story,' says Ogden, 'but I don't have to be persuaded that the sugary drinks and sweets have a negative impact on their performance and behaviour.' Patrick Holford goes further. 'Sugar is damaging the minds of our children. 'Any food containing more than 10 per cent of its calories as sugar should carry a health warning. Unless we make radical changes in the way children eat, we're in big trouble.'

· For details of FAB project, www.fabresearch.org