As ethnic variations are known to exist in inherited genetic defects, the clinico-haematological profile of Indian children with thrombophilia may be different from that of Caucasians. The aim of the study was to analyse the phenotypic and genotypic causes of thrombophilia in Indian children. Forty patients with arterial (21 patients) and venous (19 patients) thrombosis were the subjects of the study. Their age ranged from 6 days to 15 years. All of the patients were initially screened by Pro C Global assay. Activated protein C resistance (APCR) was measured. In cases with low Pro C Global values, protein C (PC), protein S (PS) and factor V G1691A, prothrombin G20210A and MTHFR C677T polymorphism were tested in all 40 cases. Of the 21 patients with arterial thrombosis, 4 (19%) had PC deficiency, 7 (33.3%) had PS deficiency and 1 (4.8%) had combined deficiency of PC and PS. Of the 19 patients with venous thrombosis, 5 (26.3%) each had PC and PS deficiency and 4 (21%) had combined PC and PS deficiency. Heterozygous factor V G1691A defect was seen in one (4.8%) patient with arterial thrombosis and three (15.8%) patients with venous thrombosis. Heterozygous MTHFR C677T polymorphism was seen in five (23.8%) patients with arterial thrombosis and in four (21%) patients with venous thrombosis. Prothrombin G20210A polymorphism was absent in all patients and controls. Protein C system defect is common in Indian children with thrombosis.