Congenital factor V deficiency is a rare bleeding disorder characterized by low coagulant activity, associated with variable phenotypic expression. Among rare inherited coagulopathies, the molecular basis of factor V deficiency is rarely described because of its relatively low prevalence in the general population. Recently, we detected two genetic variations in factor V of a Chinese patient with hereditary factor V deficiency. One was a heterozygous nonsense mutation, C67868T in exon 22, which resulted in Gln2031stop substitution in the C1 domain of factor V. The other was a previously described polymorphism, G1618A in exon10, leading to Arg485Lys substitution. We deduced that the nonsense mutation is responsible for the factor V deficiency, whereas the Arg485Lys polymorphism is expected to compensate for the low plasma factor V levels. Of note, the nonsense mutation has been confirmed to be a novel mutation.