Resistance to activated protein C (APC), which is the most prevalent pathogenetic risk factor of thrombosis, is linked to a single point-mutation in the factor V (FV) gene, which predicts replacement of Arg (R) at position 506 with a Gln (Q). This mutation modifies one of three APC-cleavage sites in the heavy chain of activated FV (FVa), suggesting that mutated FVa (FVa:Q506) is at least partially resistant to APC-mediated degradation. To elucidate the molecular mechanisms of APC-resistance and to investigate the functional properties of FV in APC resistance, FV:Q506 was purified from an individual with homozygosity for the Arg to Gln mutation. Intact and activated FV:Q506 were demonstrated to convey APC resistance to FV-deficient plasma. Thrombin- or factor Xa-activated FV:Q506 were found to be approx. 10-fold less sensitive to APC-mediated degradation than normal FVa, at both high and low phospholipid concentrations. The degradation pattern observed on Western blotting suggested that FVa:Q506 was not cleaved at position 506. However, it was slowly cleaved at Arg306, which explains the partial APC sensitivity of FVa:Q506. FV is initially activated during clotting and then rapidly inactivated in a process which depends on the integrity of the protein C anticoagulant system. During clotting of APC-resistant plasma, FV:Q506 was activated in a normal fashion, but then only partially inactivated. In conclusion, the reduced sensitivity of FVa:Q506 to APC-mediated degradation is the molecular basis for the life-long hypercoagulable state which constitutes a risk factor for thrombosis in APC-resistant individuals.