Background: Phototherapy is a commonly used treatment for neonatal hyperbilirubinemia. Hypocalcemia is a known adverse effect of phototherapy. We conducted this study to measure the efficacy and safety of head covering in prevention of phototherapy-induced hypocalcemia. Material and Methods: A total 210 newborns of >35week gestation with neonatal jaundice were included in the study. They were randomized into two equal groups- group A underwent phototherapy without any head cover while the heads of newborns in group B was covered with a cap. In both the groups, ionized serum calcium was measured at the start of phototherapy and at 48 hours. Results: The mean decline in ionized serum calcium in group A was 0.63mg/dl while in group B it was 0.34mg/dl. The incidence of hypocalcemia in the group A without head covering was 27.6 % (29 cases) while in group B with head cover was 10.5 % (11 cases). Conclusion: Phototherapy can cause hypocalcemia in a significant proportion of newborns. Monitoring of serum calcium during phototherapy is desirable to detect hypocalcemia. Use of a head cover during phototherapy appears to be a safe and effective intervention for prevention of phototherapy-induced hypocalcemia.