The monoterpene perillyl alcohol has anticancer activities that include both prevention and treatment of a wide variety of cancers in animal models. In purified enzyme studies, perillyl alcohol inhibited farnesyl-protein transferase and type I geranylgeranyl-protein transferase. However, whether and which of the polyprenyl-protein transferases is inhibited by perillyl alcohol in vivo is not known. The previously reported monoterpene-induced inhibition of the incorporation of [14C]mevalonolactone into proteins in cultured cells could be due to an inhibition of one or several enzymes in the mevalonate pathway or to changes in the levels of protein substrates for isoprenylation. In the current study, we first analyzed the levels of individual phosphorylated isoprenoid intermediates between mevalonate and geranylgeranyl pyrophosphate in NIH3T3 cells labeled for 4 hr with [14C]mevalonolactone and found that perillyl alcohol did not inhibit the synthesis of these intermediates. Next, proteins including Ras, RhoA, and Rab6 were immunoprecipitated from NIH3T3 cells. Perillyl alcohol was found to inhibit the incorporation of [14C]mevalonolactone into RhoA and Rab6 but not Ras protein. The cellular levels of these three proteins were constant over the 4-hr treatment period. Finally, the distribution of Ras, Rap1, and Rab6 proteins between the aqueous and the detergent-enriched phases was measured. Rap1 and Rab6 but not Ras from perillyl alcohol-treated NIH3T3 cells accumulated in the aqueous phase. Thus, we conclude that perillyl alcohol can inhibit the in vivo prenylation of specific proteins by type I and type II geranylgeranyl-protein transferases but not farnesyl-protein transferase in NIH3T3 cells.