The country's leading children's hospital has confirmed that organs had been removed from living babies and that some had been used for research.
The admission yesterday followed a revelation that two British hospitals had taken cash from pharmaceutical companies in exchange for thymus gland tissues removed during surgery.
Our Lady's Hospital for Sick Children in Crumlin said it was common procedure to remove the thymus gland from babies during heart surgery, but denied that the glands had been given to any pharmaceutical company for financial or any other kind of benefit.
The thymus gland is a small lymphoid organ located in the upper chest cavity, overlaying the heart. It disappears as people age but in a baby it can hinder access to the heart during cardiac surgery.
The Crumlin Hospital chief executive, Mr Paul Kavanagh, said the glandular tissues, once removed, are sent to a histology laboratory for testing. Some glands were retained for immunology research, he said.
Ms Fionnuala O'Reilly, a spokeswoman for Parents for Justice, described Mr Kavanagh's response as "inadequate".
She said that six months ago they had sought assurances and "the hospital had replied to the best of their knowledge, information and belief that no further organs had been removed".
Deputy Liz McManus, the Labour spokesperson on health, called on the Minister for Health, Mr Martin, to launch an immediate investigation into gland retention at Crumlin Hospital.