Array-comparative genomic hybridization (CGH) has emerged as a powerful new molecular tool for the high-resolution analysis of copy-number variation and breakpoint analysis. In this study, array-CGH was used to analyse known Yq deletions associated with male infertility. A microarray platform encompassing probes for chromosomes 13, 14, 21, X and Y was developed in-house and was used to detect different Yq deletion types. The successful application of this array for the detection of Yq deletions involving either the AZFb or AZFc region was demonstrated. Partial and complete AZF deletions were correctly detected in 13 patients with Yq deletions previously identified by multiplex polymerase chain reaction (PCR). This study demonstrates that array-CGH may be an alternative approach to multiplex PCR for the diagnosis of known Yq deletions and potentially a useful tool for the discovery of other Y chromosome deletions/polymorphisms associated with defective spermatogenesis.