Background: Although phototherapy has been used for more than 60 years it has some complications. The light waves produced from phototherapy reduce melatonin concentration in newborns with subsequent hypocalcemia. We aimed to assess the effect of head covering on calcium and magnesium levels in full term newborns during phototherapy.Methods: In this randomized controlled trial, 72 full-term icterus newborns weighing >2500 gr with indirect hyperbillirubinemia who received phototherapy at the phototherapy ward of Moslemin Hospital, Shiraz, southwest Iran, during March to September 2010 were recruited and divided randomly into two groups. The neonates in the case group received phototherapy while wearing a hat, while phototherapy was performed without hats for the control group. The newborns were in perfect health during the tests. The calcium and magnesium levels of each newborn were tested at baseline, and 24 hours after phototherapy and 48 after treatment. The variables were compared using Student’s t, Chi-square and repeat measurement tests.Results: 14 (38.8%) newborns in the control group and 5 (13.8%) in the case group had hypocalcemia after phototherapy. A significant difference was found between the incidence of hypocalcemia in these two groups (P=0.03). However, magnesium levels did not change significantly (P>0.05). Conclusion: Phototherapy caused hypocalcemia but it had no effect on magnesium levels. This can be prevented by covering the head during phototherapy with no need for prophylactic administration of calcium. Trial Registration Number: IRCT2013102315134N1