Background: Hyperbilirubinemia is the single most common abnormal physical finding in the first week of life and is commonly managed by phototherapy with its inherent complications. A lesser known complication of the phototherapy is hypocalcemia. Objective: To study the prevalence of phototherapy-induced hypocalcemia and to compare it between premature and full-term babies. Methods: This study was performed on 153 jaundiced neonates (62 premature, 91 full-term) that were managed with phototherapy. These neonates were completely normal on physical examination. Serum calcium was checked on arrival, 48 hours after starting phototherapy and 24 hours after discontinuation of the treatment. The first samples were considered as controls. A comparative study was made between these groups to determine the prevalence of hypocalcemia. Results: Twenty- two neonates (14.4%) developed hypocalcemia. There were significant differences between the prevalence of hypocalcemia in premature (22.6%) and full-term neonates (8.7%) (p= 0.018). None of the hypocalcemic neonates was symptomatic clinically. Serum levels of calcium returned to normal 24 hours after discontinuation of phototherapy in almost all hypocalcemic neonates. Conclusion: The study shows that neonates under phototherapy are at high risk of hypocalcemia. This risk is greater in premature neonates.