Children were subjected to invasive and inappropriate tests by doctors breaking fundamental rules as they researched the MMR vaccine, a hearing was told.
Dr Wakefield stands by his findings
Dr Andrew Wakefield, the man who first linked MMR and autism, did not have the appropriate paediatric qualifications, the General Medical Council heard.
It was also alleged he had not worked as a clinical doctor for several years.
Dr Wakefield alongside Professors Simon Murch and John Walker-Smith all deny a charge of professional misconduct.
The trio published a paper in The Lancet medical journal in February 1998 suggesting a link between the measles, mumps and rubella (MMR) jab, and bowel disease and autism.
It led to falling numbers of parents immunising their children and a row over whether the then prime minister Tony Blair had vaccinated his son Leo.
The central allegations relate to investigations for their study on 12 youngsters with bowel disorders carried out between 1996 and 1998.
At the time, all three were employed at the Royal Free Hospital's medical school in London, with honorary clinical contracts at the Royal Free Hospital.
Sally Smith QC, for the GMC, told the panel there had been a "blurring of the boundaries" between research and clinical medicine.
That led to Dr Wakefield being "very inappropriately involved in the clinical care of children when he was not paediatrically qualified", she said.
Dr Wakefield's role was as a research doctor and he had no right to investigate the children, who did not undergo proper neurological or psychiatric assessments beforehand, the GMC heard.
The three doctors did not comply with rules from the hospital's ethics committee on how the research should be carried out.
"As a result of that, very vulnerable children were subjected to inappropriate and invasive treatment," Ms Smith said.
She said the case was about the "breach of some of the most fundamental rules in medicine", including declaring conflicts of interest.
One of the key claims is that Dr Wakefield accepted £50,000 from the Legal Aid Board for research to support parents' attempts to fight for compensation.
It is alleged Dr Wakefield applied for cash so that five children and their families could stay in hospital during tests and for MRI scans for each child.
The cash was paid into an account at the Royal Free for Dr Wakefield's research, but, the GMC alleges, the cost of scans and hospital stays would have been met by the NHS.
Dr Wakefield is also accused of paying children £5 for blood samples at his son's birthday party then joking about it afterwards.
It was alleged the doctor, 50, showed "callous disregard for the distress and pain" he knew or ought to have known the children might suffer as a result of his actions.
The hearing continues.