Recently, microdeletions in the azoospermic factor region of the Y chromosome, in addition to chromosomal anomalies, have been detected in men with azoospermia or severe oligozoospermia. In this study we evaluated the molecular and cytogenetic defects of infertile men. The frequency of Y microdeletions among 105 azoospermic, 28 oligozoospermic and 32 fertile men was tested on lymphocyte DNA using a series of 20 sequence-tagged sites. In addition, microdeletions were evaluated on testicular-derived DNA among 26 azoospermic patients who underwent testicular biopsy and in whom no sperm cells could be identified. Karyotype analysis was performed on 72 of the infertile patients. Deletions were detected in 6.7% azoospermic and 3.6% oligozoospermic men. No deletions were identified among the fertile men. Identical results were obtained with DNA derived either from lymphocytes or testicular tissue. The frequency of chromosomal aberrations in the 72 infertile patients tested (62 azoospermic, 10 oligozoospermic) was 16.6%, with a high percentage of gonosome anomalies. Additional andrological parameters (hormone values, cryptorchidism) failed to identify men at risk for having microdeletions before the test. Our findings support the recommendation to perform genetic defect screening among infertile men before their enrollment in an intracytoplasmic injection/in-vitro fertilization programme.