Background: Thrombosis in neonates is rare and usually occurs as a secondary complication of underlying disease, e.g. sepsis or congenital heart disease, or exogenous triggers such as intravascular catheters. Objective: This study aimed to identify the incidence rates, risk factors and outcomes of neonates with thrombosis admitted to NICU. Patients and methods: This study was a cohort study conducted in Multiple Neonatal ICU in Sharkia Hospitals in the period from April 2020 to September 2020. The study included 24 neonates, with thrombotic disorders admitted to NICU. The included patients were subjected to careful history taking, clinical and neurological examination and laboratory investigations. Results: Three patients (12.5%) had wild mutation of factor V gene mutation while 20.8% had wild mutation of prothrombin gene mutation. All patients had MTHFR C6771 mutation. Out of them 16.7% and 83.3% had homozygous and heterozygous types .There was statistically significant relation between presence of factor V G1691 gene mutation and d-dimer, which is significantly higher in wild type mutation. Conclusion: The most important risk factor for thrombo-embolic events in neonates is placement of central catheters and some perinatal prothrombotic conditions.