Dr Andrew Wakefield insisted all tests were clinically necessary to diagnose and treat the youngsters, who were suffering from debilitating bowel diseases and autistic-type symptoms.
The academic caused a furore ten years ago when he suggested the MMR vaccination, for mumps, measles and rubella, could cause autism.
Yesterday, he told a General Medical Council disciplinary panel that the children concerned did not undergo any procedures not deemed clinically appropriate.
He claimed all the tests were ordered by the youngsters' doctor, Professor John Walker-Smith, and that all investigations were stopped when they failed to shed light on what was causing the children's problems.
He said: "At all times, our foremost consideration was the well-being of the children."
Dozens of children were put through a range of tests, including painful colonoscopies, lumbar punctures – taking spinal fluid – various brain scans and blood and urine tests.
Dr Wakefield, who is an academic and not a practising clinician, has been accused of breaking rules by ordering the tests against the patients' best interests in order to further his own research.
Dr Wakefield said: "I had no role whatsoever in deciding whether the tests should or should not take place."
He claimed all the parents knew about the research programme and were "very keen" for their children to be included.
He told the GMC panel he began studying the potential link to autism in 1995 after calls from desperate parents who said their previously normal children developed autism after the jab.
That followed his research showing a possible link between MMR and chronic bowel conditions such as Crohn's disease.
He said: "They were telling what turned out to be a remarkably consistent story of a normal child who they had lost, who had lost speech, communication, play, interaction with siblings, had sometimes become incontinent … was bloated, off their food, was losing weight, was failing to thrive."
He said the children had ultimately been diagnosed as autistic and the parents had not been able to find an explanation for what had happened.
Dozens of supporters gathered outside the hearing with banners saying "Stop the witch-hunt" and "We're with Wakefield".
Dr Wakefield, Prof Walker-Smith and their colleague Professor Simon Murch all deny serious professional misconduct. The hearing continues.
AUTISM campaigners yesterday protested outside the Scottish Parliament, demanding better services for children with the condition.
Fiona Sinclair, of the pressure group Autism Rights, said children are missing out because of a lack of specialist provision in Scotland.
She warned: "We are going to face the situation where we have hundreds of thousands of people with autism completely screwed up by the system and reaching adulthood without having had an education which meets their needs."