Background: Thrombocytopenia is frequent hematological diseases affecting neonates hospitalized to neonatal intensive care unit (NICU). Several maternal and neonatal factors contribute to thrombocytopenia development. Aim of work: To identify the incidence and possible risk factors for neonatal thrombocytopenia. Patients and methods: This prospective observational study included all newborns aged from 1- 28 days with thrombocytopenia (platelet count <150,000 /L) either full term or preterm, inborn or outborn cases admitted to NICU in Assiut University Children's Hospital from 1^st of  February 2019 to 31^st of January 2020. Thrombocytopenia frequency, as well as associated maternal risk factors as pregnancy-induced hypertension (PIH), diabetes mellitus, premature rupture of membranes (PROM), eclampsia, immunological diseases, and neonatal risk factors as sepsis, birth hypoxia, intrauterine growth retardation (IUGR), and prematurity were evaluated. Results: A total of 1590 neonates were enrolled, of them, 420 cases developed thrombocytopenia. Thrombocytopenia incidence was 26.4%. Maternal risk factors linked with neonatal thrombocytopenia were pregnancy-induced hypertensive disorders (PIH), PROM, and immune thrombocytopenia; neonatal risk factors were sepsis, prematurity, necrotizing enterocolitis (NEC), intrauterine growth retardation (IUGR), asphyxia, Toxoplasmosis, Rubella, Cytomegalovirus, and Herpes viruses infection (TORCH), and prolonged hospital stays. Among newborns with thrombocytopenia, 84.5% had late onset thrombocytopenia (> 72 hours of life). Thrombocytopenia was mild in 41.9%, moderate in 37.9%, and severe in 20.2%. Mortality rate was 20.2%. Conclusions: Thrombocytopenia frequency was 26.4% of neonates hospitalized in our NICU. The most common etiology associated with thrombocytopenia was PIH, PROM, and immune disorders, followed by neonatal sepsis, prematurity, NEC, and IUGR.