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Aim: To determine the frequency of thrombocytopenia and its severity in relation to level of indirect hyperbilirubinemia in neonates following phototherapy at tertiary care hospital. Study Design: Descriptive study Place and duration:  This study was conducted at Paediatric department (neonatal ward), Liaquat University Hospital, Hyderabad, from 1st August 2020 till 31st Jan 2021 Methodology: All neonates who fulfilled the inclusion criteria presented at pediatric department (neonatal ward), Liaquat University Hospital Hyderabad were included in the study. After written consent, brief history was taken from the mother or family member and complete blood count (CBC) was sent to check the baseline platelet count along with total serum bilirubin, it was repeated after 48 hours of phototherapy. Results: Out of 231 neonates 70 (30.3%) developed thrombocytopenia after phototherapy. In our study 117 neonates (50.6%) were males & 114 neonates (49.4%) were females with the mean age of 5.9307+1.6640 days. The thrombocytopenia was seen in 70 neonates (30.3%) and type of severity was mild, moderate & severe in 52(22.5%), 13(5.6%) & 5(2.2%) respectively. Conclusion: There was a decline in mean platelet count after phototherapy but it was not statistically significant. The treating doctor should also keep in mind, other causes of thrombocytopenia when the patient is receiving phototherapy.