Introduction: Hyperbilirubinemia (jaundice) is a common and in most cases, benign problem in neonates. Treatment options available for neonatal jaundice are phototherapy, exchange transfusion and pharmacological therapy. Hypocalcaemia is one of the know side effects of phototherapy. Objective: Effect of duration of phototherapy on serum calcium level in newborn with neonatal jaundice. Methods: Design: A prospective study Setting: A tertiary care center of Karnataka (SIMS, Shivamogga). Participants: 100 full term and 100 preterm neonates with gestational age between 34 to 42 weeks were included in study. Main outcome measures: Blood was drawn from these neonates to measure serum bilirubin and serum calcium at the time of initiation of phototherapy (0 hours) and at 24,36, 48 hours of phototherapy. Results: Incidence was 48% in preterm and 14% in term neonates. Incidence of hypocalcaemia according to duration of phototherapy being, 2 out of 24 (8%) at 24hrs of PT, 15 out of 73 (21%) at 36hrs of PT, 45out of 103 (44%) at 48hrs of phototherapy. Out of which incidence was more in preterm than in term neonates, more in SGA neonates then AGA. Incidence is not affected by sex of newborn and mode of delivery and parity of mother. Conclusion: These values show that incidence of hypocalcaemia is a significant side effect of phototherapy and more being in preterm and SGA neonates. So while starting phototherapy for neonatal jaundice, one need to be cautious about serum calcium status.