To learn more about the frequencies of congenital prothrombotic disorders in pediatric venous thromboembolism (VTE) and the outcome of this disease, we evaluated consecutive patients from 0 to 18 years with objectively diagnosed VTE at a single tertiary center over a 12-year period. We included 100 patients, with a median age at diagnosis of 1.0 year (range 2 days to 17 years). At least one underlying clinical condition was present in 96% of the patients. Factor (F)V G1691A mutation was present in 13%, FII G20210A mutation in 3%, antithrombin deficiency in 1%, protein C deficiency in 1% and protein S deficiency in 1% of the tested patients. Combined defects were present in 2.6% of the 77 patients with a complete work-up. Positive family history appeared to be the only predictor for positive testing for congenital disorders (OR 14.9, 95% CI 1.9-113). The overall mortality rate was 20%. The cumulative recurrence-free survival was 92% after 1 year of follow-up, and 82% after 7 years. The incidence and severity of the post-thrombotic syndrome was analyzed in a subgroup of 33 patients with VTE of the lower extremities. Twenty-three (70%) patients developed PTS: moderate in three and mild in 20 patients. In conclusion, congenital prothrombotic disorders seem to play a role in the development of pediatric VTE, and the risk of complications of this disease is high.