This study was conducted to identify the prevalence of FV1691A and PT20210A mutations in neonates with symptomatic thromboembolism and in healthy neonates and adults. A review of 137 healthy neonates, 368 healthy adults, and 9 neonates with clinical thrombosis was done to investigate for hereditary prothrombotic mutations. For the neonates with thromboembolism, data were collected to reveal the underlying diagnosis, site of thrombosis, and associated risk factors. Investigations included screening for factor V 1691A and prothrombin 20210A. Seven of 9 neonates had one or more risk factors at the time of thromboembolism. Seventy percent (5/7) had underlying congenital thrombophilia (4/7 FV Leiden, 1/7 homozygote protein C deficiency). Among the healthy population, 11.9% of the neonates and 9% of the adults had FV1691A mutation, 4.8% of the neonates and 2.7% of the adults had PT 20210A mutation. Incidence of FV1691A mutation in the neonates with symptomatic thromboembolism was very high. The prevalence of both FV1691A and PT20210A mutations were remarkably higher than previously reported.