Dr Michael Tettenborn, consultant paediatrician at Frimley Children's Centre and Frimley Park Hospital, Surrey, said that of 58 autistic children he had treated in the past two years, 28 had shown "definite and sustained" improvement and 15 had deteriorated again when treatment was stopped.
The children, aged from 2 to 15, were given diets free of wheat, milk or both and treated with anti-fungal remedies where necessary for skin infections such as athlete's foot.
Dr Tettenborn, presenting his findings to an Allergy Research Foundation conference in London yesterday, said: "Autism is not an end-stage diagnosis in children. Many can be helped and some returned to mainstream schooling."
His findings will fuel speculation about the causes of autism, a devastating personality disorder. Research by a team from the Royal Free Hospital, London, published two years ago, suggested that it was linked with the measles virus and could be triggered by the measles, mumps and rubella vaccination (MMR).
More recently, it has been claimed that autism was linked with the hormone secretin. But subsequent trials have failed to confirm either theory.
Dr Tettenborn conceded his findings were based on clinical observation and were not the result of a controlled trial. But he said clinical experience could be valid "if observations are made in a way that tries to reduce the effect of bias".
Simon Baron-Cohen, lecturer in psychology at Cambridge University with a special interest in autism, said experience with secretin illustrated the danger of jumping to conclusions on the basis of clinical observation alone. He said: "This is an interesting clinical observation but it needs to be treated with caution and more research is needed."