Persistent Müllerian duct syndrome (PMDS) is an autosomal recessive disorder of sex development (DSD) characterized by the presence of Müllerian duct derivatives in 46, XY phenotypic males. To date, more than 50 different mutations of the anti-Müllerian hormone gene (AMH) have been reported. Here, we report two novel mutations of AMH in a Japanese patient with PMDS. A 1-year-old male presented with bilateral cryptorchidism and normal male external genitalia. A laparoscopic surgery revealed a uterus and fallopian tubes. Serum AMH was very low. The patient's elder brother was also diagnosed as having PMDS at another hospital. Genetic analysis of AMH showed two novel mutations of p.N486T and p.V527L. Given that these two amino acids are well conserved among different species of AMH, the substitution of two amino acids might affect the normal function of AMH. In conclusion, PMDS should be included in differential diagnoses of cryptorchidism.