Isochromosome Y is one of the structural anomalies of the Y chromosome associated with a 45,X cell line and a broad spectrum of phenotypes. We present a case of de novo 46,X,+mar detected in a 17-yearold male patient. He had shortening of the right leg, bilateral breast enlargement, pubic, underarm and facial hair development, small penis and testicles, low serum cortisol, ACTH and total testosterone levels, normal LH value, high FSH value, normal testicles and epididymis, minimal left varicocele. The chromosome aberration was detected by cytogenetic analysis. Cytogenetic and molecular analysis was performed by conventional karyotyping and quantitative florescence PCR, respectively. The molecular analyses by PCR detected the presence of the SRY and AMXY genes, confirming the presence of the short arm of the Y chromosome. PCR demonstrated that the marker chromosome is of Y origin and corresponds to an authentic isochromosome for the short arm of the Y chromosome, i(Yp). We suggest that the structural alteration of the Y chromosome was a new mutation, which occurred in the initial mitotic division of the embryo, originally 46,XY. The result of accurate evaluation provides correct sex assignment and the prevention of the neoplastic degeneration of a dysgenetic gonad. The karyotype 46,X,i(Yp) indicates that the patient is preserving the SRY gene.