Congenital melanocytic nevi can be cosmetically disfiguring, give rise to melanoma, and suggest the presence of neurocutaneous melanocytosis. Management decisions must be tailored for each patient and each nevus, taking into consideration the risk for developing malignancy, risk for developing symptomatic neurocutaneous melanocytosis, cosmetic implications of having the nevus, cosmetic implications of any resultant surgical scars from their removal, adverse effects that the nevus may have on psycho-social development, and the adverse effects and long-term sequelae of any surgical intervention. The advantages and disadvantages of different modalities used in the treatment of congenital melanocytic nevi are discussed. Organizational flow diagrams are presented to help clinicians in managing patients with different sized congenital melanocytic nevi.