Structural chromosomal aberrations, such as translocations or inversions, may cause spermatogenic failure. We report a rare chromosomal anomaly 46,X,t(Y;3)(q12;p21) in an azoospermic male with normal phenotype. Twenty-two cases of a balanced Y-autosome translocation have been reported in the literature and the majority of them have been detected among azoospermic males at male infertility clinics. This structural chromosomal anomaly brings spermatogenic arrest at the primary or secondary spermatocyte.