Here we describe the case of a 35 year old male, with a harmonic phenotype, who sought medical assistance to assess the etiology of his infertility. As a result of clinical examination, karyotyping, FISH and molecular studies, we obtained the following karyotype: mos 45,X[18]/46,XY,idic(Y)q(11.2)[82]. Furthermore, the Y chromosome was characterized by the absence of the regions AZF2 (former AZFb, within the 11.22 band, and AZFc, within the 11.23 band), whereas the region AZF1 was conserved. Male infertility can be caused by several genetic alterations. Y chromosome aberrations are very frequent in infertile males. This case with an azoospermic patient carrying a complex karyotype demonstrated that cytogenetic and molecular profiling can be helpful to establish a diagnosis in cases of subjects with a normal gross phenotype.