Prenyl modification of proteins by farnesyl and geranylgeranyl isoprenoids occurs in a variety of eukaryotic cells. Culturing of Trypanosoma brucei in the presence of [ 3H]mevalonolactone (which is hydrolyzed in cells to give mevalonic acid, the precursor of protein prenyl groups) and an inhibitor of mevalonic acid biosynthesis leads to the radiolabeling of a specific set of proteins when analyzed by gel electrophoresis. T. brucei proteins were also labeled when cells were cultured in the presence of [ 3H]farnesol or [ 3H]geranylgeraniol, and each prenol labels a distinct set of proteins. Unlike mammalian cells, only a few T. brucei proteins of molecular weights similar to those of the mammalian Ras superfamily of GTPase (20–30 kDa) were labeled with [ 3H]farnesol or [ 3H]geranylgeraniol. When the 0–55% ammonium sulfate fraction of T. brucei cytosol was fractionated on anion exchange chromatography, protein farnesyltransferase (PFT) and protein geranylgeranyltransferase-I (PGGT-I) activities were detected and elute as two distinct peaks. Partially purified T. brucei PFT and PGGT-I display partly different specificities toward prenyl acceptor substrates from those of mammalian protein prenyltransferases. As shown previously, rat PFT utilizes proteins ending in CVLS and CVIM as efficient prenyl acceptors and rat PGGT-I utilizes proteins ending in CVLL and CVIM in vitro. On the contrary, T. brucei PFT farnesylates a protein ending in CVIM but not CVLS or CVLL, and T. brucei PGGT-I preferentially geranylgeranylates a protein ending in CVLL.