The prothrombin G20210A mutation has been described as the second most common genetic risk factor in thrombotic patients. Recently a new prothrombin gene variant namely prothrombin C20209T has also been found to be associated with thrombosis. In the present study the frequency of these two thrombin variants have been searched in two different groups. Group 1: A total of 377 children with thrombosis were analyzed during years between January 1997 and 2004 and screened for prothrombin G20210A mutation. Twenty-four of 387 children (6.3%) with thrombosis were diagnosed as having PT G20210A mutation. The mean age of the patients was 6.1 years (median: 6 years, range: 4 months to 17 years, 15 male, 9 female). Six of 24 children were below 2 years of age (25%). Fifteen of 24 children, (62.5%) had arterial thrombosis, most of whom (93.3%) had cerebral infarct. Group 2: The prothrombin C20209T variant has been analyzed in 200 thrombotic patients and in 200 healthy subjects. Alone of the thrombotic patients and healthy individuals carried the prothrombin C20209T variant. In conclusion, arterial thrombosis as the cerebral infarct is the most prominent type of thrombosis in children with prothrombin G20210A mutation. It seems that the prothrombin C20209T variant is not an important risk factor for the population studied.