A mutation in the factor V coagulant molecule resulting in a failure of inactivation of activated factor V by activated protein C (APC) has been recently described in 20% of adults with venous thrombosis and 40% of adults with thrombosis and a positive family history. Prevalence of the mutation in the general population in northern Europe is 2-8%. To date, there is no data regarding the prevalence of the factor V Arg506Gln mutation in children with thrombosis. We prospectively evaluated 35 children with thrombosis (20 venous, 12 non-hemorrhagic stroke, 2 purpura fulminans and 1 arterial) for activated protein C resistance (APCR). The functional assay was based on the prolongation of the activated partial thromboplastin time (APTT) by APC as described by Dahlbäck (Proc. Natl. Acad.Sci. 1994;91:1396-1400). Molecular diagnosis was performed on all children with APCR using polymerase chain reaction (PCR) amplification followed by restriction enzyme digestion with Mnl 1. Functional APCR was found in 20% (7/35) of all the children and in 35% (7/20) of the children with venous thrombosis. Five of seven (71%) children with functional deficiencies had the factor V Arg506Gln mutation. One of the children with APCR and without the factor V mutation had a lupus anticoagulant which has been described to cause APCR. The other child had acute leukemia but a lupus anticoagulant was not found. Thirty one percent(11/35) of all children had a positive family history for thrombosis. Forty five percent (5/11) of the children with a positive family history had the factor V Arg506Gln mutation. All children with the factor V Arg506Gln mutation had venous involvement, positive family history and other risk factors for thrombosis including: hyperlipidemia (2), protein S deficiency, anatomic abnormality, central venous line, lupus anticoagulant and leukemia (one each). Only one child with stroke had APCR; none had the factor V Arg506Gln mutation Our study suggests that children with thrombosis and a positive family history of thrombosis have a high likelihood of having the factor V Arg506Gln mutation and should be screened for APCR.