Aventis' French vaccine maker Aventis Pasteur confirmed that it made donations to Liverpool's Alder Hey Hospital in return for child organs.
A hospital spokeswoman said: "The hospital can confirm that for a brief period between 1991 and 1993, these (organs) were made available to a pharmaceutical company for research, and that we are aware that during that period contributions were made to the trust's cardiac department."
Aventis Pasteur admitted that donations were made in exchange for tissues over a similar period.
The latest development centres on the removal of thymus glands from children during complex heart operations at the hospital.
The removal of part or all of the gland is common practice during paediatric heart surgery so that the surgeon can get a better view of the heart. Afterwards, the gland is classed as "surgical waste".
In this case, however, they were given to Aventis Pasteur, which in return donated money to the hospital's cardiac department to cover "administrative costs".
It is thought the glands were probably used to manufacture anti-rejection drugs.