James Wisheart has voluntarily stepped down from clinical duties and as medical director of the United Bristol Healthcare NHS Trust (UBHT) to co-perate with an independent review.
There is no suggestion of any individual culpability at this stage but the investigation follows several years of controversy at the Bristol Royal Infirmary.
Mr Wisheart was one of only two surgeons to operate on babies using a complicated "switch" procedure to correct misplaced major arteries.
The operations were halted last year after an internal audit revealed higher-than-average deaths among children between 1990 and 1995.
Child surgery was transferred to the nearby Royal Hospital for Sick Children amid criticism from some parents that they would never have given permission for the surgery had they known about the mortality rate.
The trust ordered a review, which revealed friction among staff over the number of deaths but did not apportion blame.
In the wake of the findings, a separate inquiry was set up in April this year into the adult cardiac unit, which remained at the Bristol Royal Infirmary.
Preliminary findings, based on case notes of 2,500 patients 1993-1995, showed that the adult unit's overall performance was in line with the national average, the UBHT said yesterday.