Mullerian inhibiting substance (MIS), also known as anti-Mullerian hormone (AMH), causes Mullerian duct involution during male sexual differentiation and also has a postnatal regulatory role in the gonads. Serum MIS/AMH has a gonad specific pattern of expression and its concentrations are sexually dimorphic in children; hence measurement of serum MIS/AMH helps in the evaluation of children with gonadal disorders. In boys with cryptorchidism (non-palpable gonads), serum MIS/AMH correlates with testicular tissue. A measurable value is predictive of undescended testes while an undetectable value is highly suggestive of anorchia. In minimally virilized phenotypic females, MIS/AMH helps differentiate between gonadal and non-gonadal causes of virilization. In children with intersex conditions, MIS/AMH values assist differential diagnosis: a value above the normal female range is predictive of testicular tissue, while an undetectable value is suggestive of absent testicular tissue. Thus, MIS/AMH is useful for delineating gonadal pathology and facilitates the differential diagnosis and management of children with diverse gonadal disorders.