Background: Neonatal thrombosis is a rare disorder usually develops because of underlying conditions in the neonatal period, such as thrombophilia gene mutations, sepsis, congenital heart disease and surgical interventions or intravascular catheters. Objective: The goal is to look at the prevalence of neonatal thrombophilia and its risk factors among neonates admitted to the Neonatal Intensive Care Unit (NICU). Patients and methods: A cohort research that took place in neonatal ICUs in Zagazig University Hospitals from January to December 2021. Forty patients were involved. Patients were given a thorough medical history, clinical, neurological examinations, laboratory routine tests and Screening for thrombophilia gene variants by RT-PCR using the Vienna Lab Diagnostics GmbH's (FVL, PTH and MTHFR Strip Assay) ® A kit (Vienna, Austria). Results: Concerning factor V gene mutation (G1691A) there was 6 (15%) had mutations, four of them (10%) showed heterozygous and two (5%) showed homozygous s mutations while 34 (85%) were normal. Nine (22.5%) patients had mutation of prothrombin G2010A gene with five (12.5%) of them were heterozygous and four (10%) were homozygous while 31 (77.5%) were normal. As regard MTHR C677T, 10 (25%) were normal, 23 (57.5%) had heterogeneous and 7 (17.5%) showed homozygous mutations. There was statistically significant increase in D-dimer and the presence of the Factor V (G1691A) and prothrombin G20210A while it was non-significant as regard mutations of MTHFR C677T. Conclusion: Neonatal thrombosis is a critical condition. Its incidence increased with the presence of homozygous thrombophilia gene mutations especially with surgical intervention or venous catheterization.