Smith-Lemli-Optiz syndrome (SLOS) is an inherited autosomal recessive disorder resulting from defect in cholesterol synthesis due to deficiency of enzyme 7-dehydrocholesterol reductase (7-DHC). SLOS is characterized by mental retardation and associated multiple congenital anomalies including microcephaly, dismorphic facial features, syndactaly, polydactaly, hypospadias, cryptorchidism, micropenis, pelvi-ureteric junction obstruction, renal agenesis, cardiac defects (ASD, PDA, VSD etc.). Patients may also have multiple gastrointestinal, central nervous system and endocrine abnormalities. We present an unusual, unreported variant of SLOS presenting as penoscrotal hypospadias with congenital perineal hernia, multiple mesenteric lipomas in addition to other usual features of the syndrome.