Background: Phototherapy (PT) is the mainstay treatment for jaundiced neonates, regardless of the cause. Concerns about phototherapy effects on the blood and immune system have been raised with inconsistent results.   Objectives:The aim of the current work was to assess the effect of phototherapy on peripheral blood count in jaundiced neonates and determine the effectiveness of double phototherapy based on changes in hemoglobin concentration and platelet count in studied neonates. Patients and methods: This longitudinal cohort study was conducted on 60 neonates, 26 preterm (43.3%) and 34 full-term (56.7%) who had physiological jaundice treated with phototherapy. Neonates with hemolytic jaundice or direct hyperbilirubinemia, and parents refusing the assent were excluded. Venous blood samples were obtained from newborns with jaundice before PT and 48 hours after exposure to PT in all studied neonates. Complete blood count (CBC), Total and indirect Bilirubin, CRP were measured before initiating Phototherapy, 48 hours after PT for all neonates, and CBC within 5-7 days of PT for neonates with a change in blood count. The blood count before starting PT was considered the control value for individual neonates. Results:  In studied neonates, the mean age at presentation was 3.27±1.7 days and the mean weight was (2.56±0.42) kg. For all neonates after 48 hoursof PT, the mean hemoglobin concentration, RBCs, and platelet counts were significantly decreased (p < 0.05). In Full term neonates, RBCs count was significantly decreased (p < 0.01).   Among preterm neonates, RBCs and hemoglobin concentration were significantly decreased (p-value<0.01), with no significant decrease in platelet count after 48 hours of PT.  Total bilirubin inversely correlated with double PT in all studied neonates (p=0.02). Double PT also displayed a negative correlation with hemoglobin concentration and platelet count (p=0.02). This indicates that the use of double PT was associated with a significant decrease in hemoglobin and platelet count in cohorts studied. Conclusion: It could be concluded that in neonates, phototherapy causes a temporary decrease in hemoglobin concentration, RBCs, and platelet counts. Hemoglobin concentration and platelet count in newborns are important factors that would predict the ability of phototherapy to reduce bilirubin in newborns with hyperbilirubinemia. ‎