Background: Persistent Mullerian duct syndrome (PMDS) is a rare form of male 46,XY disorder of sex development characterized by the presence of Mullerian duct derivatives in otherwise phenotypically normal males. Aim: To report a novel mutation of the anti-Mullerian hormone (AMH) gene in two of three siblings with PMDS. Cases: A 2-year-old male presented with recurrent left-sided inguinal hernia and absence of right testis. Laparoscopic surgery disclosed Mullerian duct derivates and transverse testicular ectopia. AMH level was found to be low [1.6 ng/mL (normal range 7.4-373.1), 11.42 pmol/L (normal range 52.8-2663.9)]. His 15-year-old and 7-year-old elder brothers were invited, and bilateral undescended testes were noted upon examination. Female reproductive structures were identified during surgery but no transverse testicular ectopia. All cases had 46,XY karyotype. Genetic analyses could be done in two of them and a unique homozygous T to C base substitution was found at position 1591 in the AMH gene. Conclusion: This is the first report of the AMH gene mutation which is referred as p.Y531H (c.1591T>C), which resulted in different phenotypes of PMDS in three siblings.