The first was the ventilator study (described above). The second involved covert video surveillance of parents suspected of child abuse - broadcast as "Someone to watch over me", shown on Channel 4 last month - that has put him in the line of fire from families who claimed they were falsely accused.
The third study involved depriving infants of oxygen to simulate the effects of a long flight. The aim was to test claims that prolonged air travel increased the likelihood of cot death, but he was accused of putting lives at risk. Of 34 babies given air containing 6 per cent less oxygen than normal, similar to that in an aircraft cabin, four showed signs of distress and had to be given immediate extra oxygen.
Professor Southall's work in child abuse infuriated some parents who say they have been falsely accused. In an interview with the British Medical Journal last year he said he had been repeatedly threatened, his charity had been infiltrated and burgled and research grants and international aid had been blocked.
A consultant paediatrician, Colin Morley, formerly of Addenbrooke's hospital, Cambridge, who now works in Australia, described his covert videotaping of parents suspected of child abuse as a "dangerous and deceptive game".
Professor Southall is unrepentant. He told the BMJ: "No one likes a covert investigation ... It is in my opinion justified if there is no other way of identifying child abuse. "
His supporters include some of the most eminent names in the profession, who cite a landmark study of cot death conducted at the Royal Brompton Hospital, London, in the 1980s as evidence of his research pedigree. That demonstrated that apnoea, the tendency of babies to stop breathing for short periods, which had been suspected as a cause of cot death, played no role in the condition.
His supporters believe the inquiry has been made inevitable by the accusations of his enemies and will clear his name.
His detractors believe that his readiness to court controversy and to press research to its ethical limit was demonstrated in the study in which babies were deprived of oxygen. The North Staffordshire Hospital's own research ethics committee initially rejected the proposal because of fears about the possible danger to the babies involved.
It later relented after reassurances from Professor Southall that a paediatrician would be on permanent standby and there would be no coercion of parents to allow their babies to take part.