Up to 100,000 brains were illegally retained for decades without the knowledge of the dead person's relatives, a government inquiry revealed yesterday.

More than 20,000 of these illicitly obtained brains are still in storage for use in medical research, but tens of thousands of others were destroyed after they were dissected by medical students or had served their purpose in experiments.

The Department of Health's chief medical officer, Sir Liam Donaldson, said: "I'd like to express my most sincere apologies to the Isaacs family for the distress these events have caused and to all other families affected by issues raised in the report.

"I would like to thank Mrs Elaine Isaacs for campaigning to draw the circumstances of her husband's case to public attention and to enable the important issues that it raises to be independently reviewed.

"Removing organs or tissues at post mortem examination without lawful authority is an affront to families who have lost a loved one. I can assure them and other families that, since the time of the activities described in this report, the practice of routine retention and use of organs and tissue without consent is no longer acceptable practice in the NHS.

"It is important that public confidence in bona fide medical research that has been subject to proper ethical review and approval should not be adversely affected by the findings in this report which relate to unacceptable practices from a past era. We cannot find solutions to the major disease problems of the 21st century without high quality medical research but we must have the support of patients and the public, and the consent of the families directly involved.

"Her Majesty's Inspector of Anatomy, Dr Jeremy Metters, is to be commended on the meticulous investigative work that he has carried out in pursuit of the facts in this case. We shall consider his recommendations carefully and then respond more formally.

"I hope that this report will bring the family of Mr Isaacs some measure of peace in the knowledge that the concerns they raised have now been fully and independently investigated with the thoroughness that they required.

"Seeking patient or family consent for research on organs retained at post mortem is not an optional extra but a legal requirement and an essential feature of good clinical practice. We intend to enshrine the changes that we have already made and to make further reforms through new legislation that will clarify any past misconceptions. The Inspector's additional findings are particularly timely in this respect and we will be bringing forward a new Human Tissue Bill, relating to both adults and children, as soon as parliamentary time allows."

Forum Response: Sane

Marjorie Wallace, head of Sane, told ePolitix.com: "While it is essential that there are clear directions and consent for relatives, our concern is that the emotions surrounding this and previous inquiries have already almost killed post-mortem research into illnesses such as schizophrenia and depression.

"There is an acute shortage of brain tissue, and many of those carrying out the research feel so stigmatised that they have ceased investigations. It was post-mortem research which led to the discovery of L-Dopa for Parkinson's and drugs for Alzheimer's.

"There is now a danger that similar progress will not be made on treatment for mental illness. We would call for a revival of organised brain banks and systems such as donor cards so that those who suffer now are encouraged to leave their brains to prevent suffering in the future."

Forum Response: Depression Alliance

Jim Thomson, director of the Depression Alliance, told ePolitix.com: "Research into depression and other mental illness is vital. However, of equal importance are the legal and moral considerations when dealing with human tissue.

"Clearly, current rates of organ donation do not meet research needs but the negative publicity arising from the Isaacs Report can only serve to encourage stigma around mental illness and discourage future organ donations. In the final judgement, any benefits gained from these illicit practises have been more than negated by the harm caused."

Forum Response: Council of Heads of Medical Schools

A spokesman for the CHMS told ePolitix.com: "It would be inappropriate for the Council of Heads of Medical to comment on individual cases and CHMS regrets any distress caused to the relatives of those who have died. Nonetheless CHMS particularly welcomes the positive statements in the Isaacs Report recognising the essential nature of post-mortem research, the risk to future research potential and the critical importance of regaining public confidence in this research.

"Post mortem research on the brain is essential for future improvements in prevention and treatment of neuropsychiatric diseases and to improvements in patient care. There is no alternative to post mortem study for continued progress in the understanding of disease processes that affect the brain. The importance of this field of research cannot be over-emphasised."