The present study was aimed to assess the effect of head covering on phototherapy induced hypocalcaemia in jaundiced term newborns. This study was conducted in a medical college hospital in South India. All enrolled term neonates were randomly allotted to either the group using a cap (cases) or the group not using a cap (controls) by using closed envelope method. Conventional phototherapy equipment was used and the American Academy of Pediatrics (AAP) guidelines for phototherapy were followed. Serum calcium levels were measured before and after 24 hours and after 48 hours of phototherapy in case phototherapy was continued for a longer period. Results were tabulated and analyzed using student t-test and Chi square test. Out of 110 newborns studied, 58(53%) were boys and 52(47%) were girls. The average age of onset of jaundice was between 25- 48 hours. The mean weight of the neonates was 2993±241g. Mean total serum bilirubin level before phototherapy was 13.43±3.27mg/dl. Mean total serum calcium level before phototherapy was 9.92±0.84mg/dl. Mean total serum calcium levels after 24 hours of phototherapy were 9.37±0.67mg/dl and 9.21±0.71mg/dl in cases and controls respectively (p =0.000). Mean total serum calcium levels after 48 hours of phototherapy were 8.87±0.80 mg/dl and 8.52±0.54mg/dl in cases and controls respectively (p=0.022). Only 3 babies in control group developed hypocalcaemia (Serum calcium <8 mg/dl) and none were symptomatic. There is a reduction in the total serum calcium level after phototherapy which is more as the duration of phototherapy is increased. The reduction in the total serum calcium level after phototherapy is significantly less when the head is covered with a cap during phototherapy than when it is not.