Fraser syndrome is a rare disorder with autosomal recessive inheritance. Neurodevelopmental retardation, craniofacial anomalies such as abnormal hairline, low nasal bridge, hypoplastic notched nares, cleft lip/palate, teeth crowding, cryptophtalmos, external/middle ear anomalies, and larynx malformations, umblical hernia, genitourinary system anomalies, such as clitoral hypertrophy and renal agenesis, and skeletal system anomalies, such as syndactyly are among the common findings of the syndrome. Physical examination of a 16-month-old girl, referred for neurodevelopmental delay and multiple congenital anomalies revealed motor and mental retardation besides multiple dysmorphic features and a perineal fistula with subclitoral opening. Ultrasonograpy showed a pancreatic cyst, left kidney agenesis, but no gonadal structures were present. Cerebral MRI revealed ventricular dilatation and Sylvian fissure atrophy. Chromosome analysis resulted in normal 46,XX female karyotype. Based on clinical findings, Fraser syndrome diagnosis was made. Novel features, such as perineal fistula, pancreatic cyst and Sylvian fissure atrophy in the present case support the proposed clinical variability of the Fraser syndrome. In this case report, we aimed to present our patient's clinical findings and evaluate the genetic basis of Fraser syndrome.