Introduction. The problem of neonatal thrombosis is becoming increasingly urgent in clinical practice due to its importance in the development of a complicated course of the neonatal period in children with hereditary and acquired thrombogenic risk factors. The aim of the investigation is to present a clinical case of multiple thromboses in a premature newborn infant with congenital heart disease on the background of multigenic thrombophilia, complicated by neonatal sepsis. Materials and methods. Materials for the investigation were the primary medical records: history of the newborn, medical history of the patient-newborn child with the established diagnosis of great-vessel thrombosis, with the congenital heart disease and the presence of genetic thrombophilia, who was under observation for 2 months. The findings of objective, laboratory (clinical blood tests, investigation of hemostasis parameters, homocysteine concentration, molecular-genetic study of hemostasis enzymes genes, folate cycle enzymes genes) and instrumental (CT angiography, ultrasonic examination of abdominal cavity and retroperitoneal organs, ECHO cardiography, ultrasonic Dopplerography) research methods were evaluated. Results and Discussion. In the clinical observation under consideration, there was a burdened molecular genetic background consisting of carriage of plasminogen activator inhibitor gene polymorphisms and folate cycle enzyme genes: MTHFR 677 – C/T, MTHFR 2756 – A/G, MTRR 66 – G/G, and hyperhomocysteinemia were the factors responsible for multiple thrombosis in a patient born with critical congenital heart disease (CHD), contributed to generalization of the infection process with the development of multiple organ failure, and exacerbated the postoperative period after correction of heart disease. Conclusion. The clinical case demonstrates the development of multiple thrombosis and septic process in a child born with CHD. The results of molecular genetic study proved the presence of hereditary thrombophilia in the child, which was a predictor of thrombosis development and probably a risk factor aggravating the severity of generalized infectious process, which complicated pre- and postoperative periods of the main disease, CHD.