Sex chromosomal mosaicism has been considered as a major cause of human sexual differentiation disorders, like partial virilization and ambiguous genitalia. 45,X/ 46,XX, 45,X/46,XY and 46,XY/47,XXY are three most common sex chromosome mosaics associated with human ambiguous genitalia. Here, we report the case of a 3-year-old boy with ambiguous genitalia, bilateral cryptorchidism, and with an inguinal hernia. G banded cytological karyotyping and FISH analyses revealed that the patient has extremely rare and novel sex chromosome mosaic 45,X/45,Y/46,XY/46,YY/47,XYY karyotype. These cells exist in different percentages, important for phenotypic appearance of the patient. This is a first report of an unusual mosaic karyotype causing ambiguous genitalia.