A feasible method was developed to determine the stereochemical direction of the C-C bond formation with respect to the face of the double bond of isopentenyl diphosphate in the prenyltransferase reactions. This method was applied to the reactions of undecaprenyl diphosphate synthase and heptaprenyl diphosphate synthase, which catalyze (Z)-prenyl chain elongation and (E)-prenyl chain elongation, respectively. In both cases, the C-C bond formation was found to take place at the si face of the double bond with elimination of one of the hydrogens of C-2 in a syn fashion.