We investigated the frequency of copy number variations (CNVs) in the Y chromosome of Japanese children with hypospadias. We analyzed the copy number of the azoospermia factor (AZF) region and SRY, using multiplex ligation-dependent probe amplification. Four AZF-linked CNVs, including one novel simple duplication, were identified in 39 of 89 patients, at a frequency comparable to that of those in unaffected individuals. SRY-linked CNVs were absent in our patients. The results imply that CNVs in the AZF region and SRY are not associated with the risk of hypospadias in the Japanese population, although the pathogenicity of the AZF-linked simple duplication remains to be elucidated. (C) 2016 S. Karger AG, Basel