Unilateral or bilateral cryptorchidism is found in 80-100% of male patients with Prader-Willi syndrome (PWS). Recently, the relationship between Yq deletions and cryptorchidism has been assessed. However, the relationship between Yq deletions and PWS patients with cryptorchidism remains unclear. Polymerase chain reaction (PCR) amplification of 51 DNA loci encompassing all of the regions for azoospermia factor (AZF) of the Y chromosome, including the deleted in azoospermia (DAZ) and ribonucleic acid-binding motif (RBM) genes, were examined for microdeletions in 10 PWS males with cryptorchidism and 20 healthy control male subjects. No microdeletions of 51 loci were found in any of the PWS males. The present study therefore suggests that microdeletions in the AZF regions of the Y chromosome do not relate to the occurrence of cryptorchidism in PWS patients.