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: This study was conducted on 50 full-term jaundiced neonates (23 males & 27 females) 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. Results: In our study hypocalcemia was assessed as a complication of phototherapy in newborns managed for neonatal hyperbilirubinemia as mean calcium was 8.63 ± 1.54 mg/dl pre-phototherapy and was 8.22 ± 1.64 mg/dl postphototherapy. The difference was as statistically significant (p < 0.001). Calcium level was lower after phototherapy. Pre-phototherapy, 12 (24.0%) showed hypocalcemia (< 8 mg/dl) and 38 (76.0%) showed normal calcium (> 8 md/dl). Post-phototherapy, 19 (38.0%) showed hypocalcemia (< 8 mg/dl) and 31 (62.0%) showed normal calcium (> 8 md/dl). The difference was as statistically significant (p = 0.039). Hypocalcemia was higher after phototherapy. Whereas, mean Mg was 2.25 ± 0.32 mg/dl pre-phototherapy and was 2.03 ± 0.38 mg/dl post-phototherapy. The difference was as statistically significant (p < 0.001). Mg level was lower after phototherapy. Pre-phototherapy, 11 (22.0 %) showed hypo and 39 (78.0 %) showed normal. Post-phototherapy, 17 (34.0 %) showed hypo and 33 (66.0 %) showed normal. The difference was as statistically non-significant (p = 0.238). Conclusion: Hypocalcemia is a common complication of phototherapy whereas hypomagnesaemia cannot be considered as a complication of phototherapy.