A 1-year-old boy was referred to us because of abnormal external genitalia; that is, his penis was kinked toward the perineal region. We diagnosed hypospadias. Chromosomal examination was performed on a sample of peripheral blood, the karyotype was 46,X+mar. Detailed karyotypic analysis revealed that the short arm of the marker chromosome originated on the ninth chromosome, but we could not determine whether the long arm was part of the Y chromosome, even with the use of quinacrine mustard. The sex-determining region of the Y was detected using the polymerase chain reaction method, which suggested that the long arm of the marker chromosome was delivered from the short arm of the Y chromosome.