Methods: Twenty newborns that received femoral artery catheterization within 6-month period were enrolled in this study. Blood samples were taken for complete blood count, prothrombin, activated partial thromboplastin time, INR ratio and mutations of factorV Leiden, prothrombin 20210A, methylenetetrahydrofolate reductase C667T and A1298 before the procedure. 100 U/kg bolus of heparin was infused during catheterization. 28 U/kg/hour infusion of heparin was given to the patients with clinically suspected thrombosis during first few hours after catheterization. Doppler ultrasonography was performed in all patients within 6 hours after catheterization. Results: The gestational age of patients ranged from 31 to 40 weeks (median 39). Mean birth weight was 2996 ± 589 (1880-4000 gr). Arterial thrombosis was detected in 10 patients by Doppler USG. On development of arterial thrombosis, patient age, gender, diagnosis, treatments, platelet count, hemoglobin, prothrombin and activated partial thromboplastin time values, FactorV Leiden, prothrombin 20210A, methylenetetrahydrofolate reductase C667T and A1298 mutations were found as not impacting (p>0.05). Those who were found to have thrombosis in Doppler ultrasonography had lower INR levels compared to others (p= 0.023).