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 <i>SRY</i>, 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. <i>SRY</i>-linked CNVs were absent in our patients. The results imply that CNVs in the AZF region and <i>SRY</i> 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.