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Abstract Background Neonatal sepsis is the major cause of morbidity and mortality in neonates. Frequency of bacterial sepsis is affected by seasonal variations. This study was done to rule out the effects of seasonal variation on neonatal sepsis and to determine isolated bacterial agents and their antibiotic sensitivity profile. Results This cross-sectional study included100 neonates with suspected sepsis, and conducted during summer and winter seasons. High frequencies of neonatal morbidities were observed like poor feeding (98%), Jaundice (82%), pallor (76%), respiratory distress (66%) and convulsions (64%) in winter, whereas fever (40%) and edema (12%) in summer. Statically significant correlation was found between the seasonal variations and different symptomatic expression of bacteremia like jaundice, respiratory distress, convulsions and poor feeding (p value