The aim of this study was to analyse ethical issues concerning the storage of human biological samples to be used in genetic analyses and pharmacogenetic research based on a French experience of DNA banking in a cohort of human immunodeficiency virus (HIV)-infected patients started on a protease inhibitor-containing treatment. We describe the ethical issues raised during the establishment of a DNA bank, including questions dealing with autonomy, benefit to the patient, information sharing and confidentiality as well as guarantees concerning the storage and use of DNA. The practical applications of themes illustrated theoretically in the literature are discussed. Most of the points raised are not specific to HIV, but some of them may be more accurate due to the characteristics of the HIV population, which is more involved in the social debate through the community life and the increased risk of stigmatization. Our results are summarized in the memorandum and consent form presented in the Appendices. One issue still open to discussion is the way the results of genetic data will be given to the patients. This work should allow other researchers and members of evaluation committees to enrich their considerations and should stimulate discussion on this topic.