We describe a case of mosaic Klinefelter syndrome demonstrating an isodicentric Y chromosome. A 70-year-old man visited our outpatient clinic complaining of dysuria resulting from atrophy of the penis. His height was 170 cm and his weight was 60 kg. A serum hormonal analysis revealed hypergonadotropic hypogonadism. A chromosomal analysis with fluorescence in situ hybridization revealed four cell lines in which the karyotypes were 47,XXY, 46,XY, 46,XX and 47,XX,idic(Y) (q11.2). To the best of our knowledge this is the first case of mosaic Klinefelter syndrome bearing an isodicentric Y chromosome. The origin of the isodicentric Y is discussed.