Andrew Wakefield was found guilty of serious professional misconduct at a hearing in central London.
The 53-year-old, who is currently in New York, is expected to appeal against the decision, which is effective within 28 days.
A GMC panel ruled Dr Wakefield acted in a way that was "dishonest", "misleading" and "irresponsible" while carrying out research into a possible link between the measles, mumps and rubella (MMR) vaccine, bowel disease and autism.
Furthermore, he "abused his position of trust" and "brought the medical profession into disrepute" in studies he carried out on children.
In a statement, Dr Wakefield said: "In reporting their findings the GMC panel sought to deny that the case against me and my colleagues is related to issues of MMR vaccine safety and, specifically, the role of this vaccine in causing autism.
"This is not in fact the case.
"Efforts to discredit and silence me through the GMC process have provided a screen to shield the Government from exposure on the (Pluserix) MMR vaccine scandal."
Another doctor involved in the research, Professor John Walker-Smith, 73, was also found guilty of serious professional misconduct and struck off the medical register.
A third doctor, Professor Simon Murch, was found not guilty.
Video: MMR doctor struck off
Dr Wakefield caused controversy when he published a study suggesting a link between the MMR vaccine, bowel disease and autism.
The research, which appeared in The Lancet medical journal in 1998, sparked a massive decline in the number of children given the triple jab.
Today, the GMC described how Dr Wakefield took blood from his son's friends at a birthday party, paying the youngsters £5 each, before joking about it during a US presentation in March 1999.
"In causing blood samples to be taken from children at a birthday party, he callously disregarded the pain and distress young children might suffer and behaved in a way which brought the profession into disrepute," panel chairman Dr Surendra Kumar said.
Dr Wakefield ordered some youngsters to undergo unnecessary colonoscopies, lumbar punctures (spinal taps), barium meals, blood and urine tests and brain scans.
Yet most of the children did not meet the criteria for inclusion in the research, the GMC ruled.
Furthermore, Dr Wakefield and profs Walker-Smith and Murch did not have ethical approval to investigate them.
The GMC ruled that Dr Wakefield submitted an application for funding from the Legal Aid Board for research but failed to disclose that some of the costs would have been met by the NHS anyway.
Dr Wakefield was an honorary consultant in experimental gastroenterology at London's Royal Free Hospital at the time of his research, yet he breached its terms by clinically managing patients, the GMC said.
Dr Kumar said: "In all the circumstances and taking into account the standard which might be expected of a doctor practising in the same field of medicine in similar circumstances in or around 1996 to 1998, the panel concluded that Dr Wakefield's conduct not only collectively amounts to serious professional misconduct over a timeframe from 1996 to 1999 but also, considered individually, constitutes multiple separate instances of serious professional misconduct."
The GMC hearing, which lasted 217 days, heard from 36 witnesses and cost more than £1 million, is the longest in the GMC's history.
Regarding Prof Murch, Dr Kumar said he should have ensured there was appropriate ethical approval for research on the children.
But he said the doctor brought carrying out lumbar punctures to an end and his involvement was subsidiary to, and more limited than, that of Dr Wakefield and Prof Walker-Smith.
Professor Terence Stephenson, president of the Royal College of Paediatrics and Child Health (RCPCH), said the suggestion of a link between autism and MMR had done "untold damage" to the UK vaccination programme.
In a statement, Prof Walker-Smith said he was considering today's decision.
He added: "I am devastated that the GMC has decided to erase me from the medical register.
"At each stage of the GMC's investigation and hearing I have put forward strong evidence contesting the central allegations against me.
"It is deeply disappointing that the GMC has chosen to impose a sanction of such severity despite the evidence they had available to them.
"I have always and will continue to vigorously contest any suggestion of wrongdoing on my part.
"For 40 years I dedicated my career to paediatric gastroenterology and am proud of the worldwide recognition I have received from my peers in the medical community.
"I have always been committed to the care of children and my first concern has been to do the best for them."
Prof Murch said the GMC investigation was "prolonged and difficult".
He added: "As a paediatrician I am committed to the care of children and my first priority has always been to deliver the highest standards of care to them.
"I look forward to continuing with my work and to putting this matter behind me once and for all."
Some of the parents of autistic children treated by the three doctors described the decision as "shameful" and said Dr Wakefield and Prof Walker-Smith were "good caring doctors".
In a statement, they said no parent had complained to the GMC and claimed children's medical data had been obtained in contravention of the Data Protection Act.
"Not one of The Lancet 12 children or their parents was given legal aid to represent their interests at the hearing," the statement added.
"The GMC based its unjust case against the doctors on the wrong ethical approval, which was submitted after and not before The Lancet work began.
"The three doctors claim that the correct ethical approval was granted in 1995 not 1996 and have the letter of proof.
"Because of this gross injustice the doctors have lost their right to practice and yet they have not harmed one single patient.
"Indeed the children vastly improved under their care."
The statement went on: "This scandalous show trial was used to mask the real concerns parents have about why their children regressed into autism following MMR.
"The GMC's real intention has been to discredit research which, if allowed to continue, could implicate the MMR in the alarming rise in the numbers of autistic children."
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