A patient presenting with azoospermia was referred for genetic evaluation, and upon karyotyping, he was revealed to have two cell lines—mos46,X,ider(Y)(q10)inv(Y)(p11.3q11.1)/45,X. Further cytogenetic studies such as C banding and fluorescence in situ hybridization were performed, which revealed an inversion duplication of a segment of the Y chromosome; hence, the derivative chromosome contained two SRY genes but only one centromere. Y chromosome microdeletion studies were performed in select STS sequences of AZFa, AZFb and AZFc regions and found to be negative for microdeletions. For such a case of infertility, the couple was advised to undergo artificial reproductive techniques with the help of donor spermatozoa.