Background: Late-onset sepsis (LOS) is well-defined as onset of sepsis more than 72 hours of age. Late onset thrombocytopenia occurs frequently due to sepsis. Objective: The aim of our study was to learn the incidence of thrombocytopenia in neonates with late onset nosocomial sepsis and to study the effects of different infectious organisms on platelet counts and thrombopiotin (Tpo) Level in Neonates with LOS. Methodology: This study was performed prospectively on 60 neonates from Neonatal Intensive Care Unit (NICU). The sample eligibility criterion was the presence of documented nosocomial late onset sepsis (LOS). Sixty non septicemic neonates from the same NICU were included in the study as a control group. All neonates were subjected to the following: Complete blood cell count, C-reactive protein assessment, blood culture and assesment of thrombopoietin level. Results: Our study showed that platelet counts were significantly lower among case group compared with control group (p<0.01). This study showed that more than half of the cases had severe thrombocytopenia (53.13%) and the majority of them had bacteria culture test positive (83.3%) with high mortality among them (53.13%). The most common isolated organism was klebsiella pneumoniae followed by Staph. aureus then Coagulase Negative Staphylococcus (CONS). In our study, there was statistically significant association between platelet count in thrombocytopenic neonates and blood culture resultes among studied cases. There was significant inverse correlation between platelet count and Tpo level in thrombocytopenic group. Conclusion: Thrombocytopenia is an early marker of sepsis and can be used as a screening procedure for early detection of sepsis, especially in NICU. Type of organism in blood culture results affect both platlet count and Tpo level.