In an extraordinary outburst, Janardan Dhasmana told the public inquiry he had been professionally and financially ruined by the tragedy at the Bristol Royal Infirmary.
But he added: "Whatever suffering I have gone through is no match to the suffering of losing a child. I am not a cavalier surgeon. I did not and I do not risk any patient's life unless I believe fully I can benefit them. Unfortunately it didn't work. I wish I had not operated on those children."
In a voice trembling with emotion, he said: "I never believed in using patients as guinea pigs. I followed the practice at the time as I saw my elders and seniors doing.
"I do not consider myself an incompetent doctor and I hope the inquiry finds that out. My results, barring the arterial switch, should speak of myself as a surgeon."
As his wife sobbed in the public gallery, he added: "My family life has gone and I have lost confidence in myself. This is the first time in two years I have been able to speak to an audience."
Mr Dhasmana was found guilty of serious professional misconduct by the General Medical Council last year and banned from operating on children for three years. The Bristol Royal Infirmary later sacked him but he is appealing against his dismissal.
The GMC case focused on 53 cases, in 29 of which the baby died or was brain damaged. The public inquiry is now investigating almost 1,900 complex heart operations carried out at the infirmary between 1984 and 1995.
Yesterday was the last of four Mr Dhasmana has spent on the witness stand, during which he described how the first five children on whom he had performed a complex heart operation known as an "arterial switch" had all died.
"Why did I go on doing it? I wish I had not, I wish I had a crystal ball," he said. "I was asking for help all the time. The arterial switch, I was not the one who was really just doing it and not telling anybody. I was doing it and then asking people - what has gone wrong?"
He said warning letters about the paediatric unit's high death rate had been "flying round" the department but he had not been put in the picture. Then colleagues he had worked with for 20 years abandoned him. "I was dropped like a bullet from a very high place," he said.
Asked by Brian Langstaff QC, for the inquiry, if he was upset to lose the work in 1995, he replied: "Very much so. My records were improving in the last five years and, except for the arterial switch, were better than average in the country.
"I was an above-average paediatric cardiac surgeon. I was being asked to leave paediatric cardiac surgery mainly in response to media pressure. That upset me, but my adult work did not suffer.
"I was the number one or two surgeon out of four in adult work and I was upset, I felt it was taken away from me."
The inquiry was adjourned until Monday.