Background: Neonatal hyperbilirubinemia is one of the most common newborn entities. phototherapy has been the therapy of choice for neonates suffering from indirect hyperbilirubinemia. One of the consequences of phototherapy is hypocalcaemia and hypomagnesaemia. Phototherapy leads to inhibition of pineal gland by transcranial illumination resulting in a decline in melatonin level which leads to increased calcium absorption by bones. Patients and Methods : The present study was conducted on 50 full-term jaundiced neonates (23 males &27females) received phototherapy for treatment of neonatal indirect hyperbilirubinemia. Cases were selected from those admitted to NICU of Benha University hospital. serum calcium, serum magnesium were measured in their blood samples before phototherapy and after 48 hours and at the end of phototherapy. Data were fed to the computer and analyzed using IBM SPSS software package version 20.0. Results: In our study hypocalcemia was assessed as a complication of phototherapy ±in newborns managed for neonatal hyperbilirubinemia as mean calcium was 8.63 1.64 Post phototherapy. The difference was as ±1.54 Pre phototherapy and was 8.22 statistically significant (p