Idiopathic Sertoli cell-only syndrome (SCOS) is characterized by azoospermia, small testes, absence of germ cells in the testes, elevated follicle stimulating hormone and normal testosterone concentrations. The Y-chromosome is involved in the regulation of spermatogenesis and in the pathogenesis of a fraction of idiopathic male infertility. An azoospermia factor (AZF) is present on the Y-chromosome long arm euchromatic region (Yq11) and two gene families (DAZ and RBM) have been identified within this region. The aim of this study was to investigate whether a specific pattern of Yq11 microdeletions may be associated with idiopathic SCOS. Eighteen idiopathic subjects showing a testicular cytological picture of bilateral SCOS were selected and tested by polymerase chain reaction for a set of 29 Y-specific sequence-tagged sites (STS). We found Yq microdeletions in 10 out of 18 patients (55.5%) while the fathers or brothers of six out of 10 patients deleted for Yq were shown to carry an intact Y-chromosome. These deletions may therefore be considered as de-novo deletions and the cause of SCOS. The analysis of the microdeletions allowed us to identify two homogeneous regions that have a high incidence of deletion. The smallest deletion, common to all patients, is located in Yq interval 5. We therefore speculate that there is a relationship between specific, well-characterized Yq11 microdeletions and a testicular picture of SCOS, identifying an Y-related region frequently deleted in this syndrome. In conclusion, the findings of this study demonstrate that a large percentage of idiopathic SCOS may be genetically determined and identify an Y-related region that seems to possess one or more still unknown genes essential for spermatogenesis.