A young male with a 45, X/46, X, r(Y)/47, X, r(Y), r(Y)/48, X, r(Y), r(Y), r(Y) karyotype was described. The phenotype was substantially characterized by short stature (< 3rd centile) and by a scrotal hypospadias with a normal sized penis. Fluorescent in situ hybridization (FISH) and molecular analysis by X and Y chromosomes specific probes were performed to identify the origin of the marker chromosomes which had been impossible to define by conventional and high resolution cytogenetics techniques. Small rings was identified as Y-derived ring chromosomes, lacking the entire heterochromatic portion of the long arm and the very distal tip of the short arm. The correlation between the phenotype and the chromosome constitution of the propositus was discussed.