Factor V Leiden (FVL) R506Q and Prothrombin G20210A are clinically important genetic mutations associated with increased susceptibility to venous thrombosis. The objective of our study was to design a polymerase chain reaction/restriction fragment length polymorphism (PCR/RFLP) reaction that allows simultaneous detection of these two mutations. The reaction can be used in routine diagnostic settings. We have analysed 4504 alleles for each mutation with a mutagenic primer-based PCR system with a low failure rate. The system eliminates the false positive FVL G1691A results associated with other PCR/RFLP caused by rare confounding mutations adjacent to restriction endonuclease recognition sites. This multiplex PCR/RFLP reaction is rapid, robust and dependable.