The pathogenic mechanisms by which varicocele disrupt spermatogenesis are not clearly understood and it is possible that when varicocele is associated with a severe bilateral testiculopathy, other causes may represent the actual aetiological factor. Since microdeletions in the Y chromosome long arm (Yq) have become in last years a major cause of male infertility, we perform a Yq microdeletion screening in infertile men with varicocele. We selected 40 patients with severe oligozoospermia (sperm count<5x10(6)/ml, group 1) and 80 with varicocele and mild oligozoospermia (sperm count 10-20x10(6)/ml, group 2). Deletions of Yq was observed in seven out of 40 patients (17.5%) of group 1, while no deletions were found in patients of group 2, suggesting that the bilateral testicular damage observed in patients of group 1 is due to the underlying genetic anomaly, and not to varicocele itself. The finding of a genetic aetiology in infertile men with varicocele suggests that in such patients a Yq microdeletion screening should be performed, both for a proper diagnosis and to avoid unnecessary treatments that will probably not improve the sperm count.