Intracytoplasmic sperm injection (ICSI) is a successful treatment option for severe male infertility, although the aetiology of the disorder remains unclear in most cases. Recently, microdeletions in the AZF region of the Y chromosome have been detected in men with azoospermia or severe oligozoospermia. In this study we investigated the prevalence of microdeletions in the AZF region of the Y chromosome in a population of men undergoing ICSI, and looked for clinical characteristics of men with and without this deletion. Blood was drawn from 164 men, who were on the waiting list for ICSI treatment: 19 were azoospermic, 111 oligozoospermic and 34 normozoospermic (after previous total fertilization failure). A total of 100 men with proven fertility served as a control. Microdeletions in the AZFc region were present in seven of the 111 oligozoospermic men (6.3%). Compared with oligozoospermic men without microdeletions, men with microdeletions had a lower concentration of follicle stimulating hormone (FSH), a lower number of motile spermatozoa and a lower frequency of abnormal findings at andrological history or examination. No microdeletions were found in the azoospermic, normozoospermic and control groups. In conclusion, microdeletions in the AZFc region are relatively frequently found in men with severe unexplained oligozoospermia. In the ICSI era this finding has an important impact because this form of male infertility is now potentially hereditary. Therefore we recommend DNA screening (and genetic counselling) before ICSI, especially in men with normal FSH, severe oligozoospermia and no abnormal clinical andrological findings.