OBJECTIVE To determine whether cryptorchidism associated with azoospermia or oligozoospermia may be due to microdeletions of the Y chromosome. METHODS Controlled clinical study. METHODS Division of Medical Genetics and the Andrology Centre, Department of Obstetrics and Gynecology, University Medical Center, Ljubljana. METHODS Ninety men from infertile couples (36 azoospermics, 35 oligozoospermics, and 19 normozoospermics) with a medical history of cryptorchidism. Nineteen excryptorchid patients with cryptorchidism and Y chromosome microdeletions among 3099 patients from 14 publications. METHODS Collection of semen and blood samples. METHODS Medical history, testicular volume, sperm characteristics, serum FSH levels, testicular histology, presence or absence of Y chromosome microdeletions, including all known Y chromosome genes/gene families in the azoospermia factor (AZF) region. RESULTS Deletions of the Y chromosome were found in 2 out of 71 cryptorchid patients with azoospermia or oligozoospermia (2.8%). The literature review showed that the incidence of microdeletions in infertile patients with cryptorchidism is lower in comparison with the general population of infertile men (4.9% vs. 8.1%), and that the frequency of cryptorchidism in patients with Y chromosome deletions (6 out of 103, 5.8%) is significantly lower in comparison to infertile patients without deletions (178 out of 1141, 15.6%). CONCLUSIONS No causal relation exists between Y chromosome microdeletions and cryptorchidism.