We have recently demonstrated that mevalonate kinase and farnesyl diphosphate (FPP) synthase are localized predominantly in peroxisomes. This observation raises the question regarding the subcellular localization of the enzymes that catalyze the individual steps in the pathway between mevalonate kinase and FPP synthase (phosphomevalonate kinase, mevalonate diphosphate decarboxylase, and isopentenyl diphosphate isomerase). These enzyme are found in the 100,000 ؋ g supernatant fraction of cells or tissues and have been considered to be cytoplasmic proteins. In the current studies, we show that the activities of mevalonate kinase, phosphomevalonate kinase, and mevalonate diphosphate decarboxylase are equal in extracts prepared from intact cells and selectively permeabilized cells, which lack cytosolic enzymes. We also demonstrate structure-linked latency of phosphomevalonate kinase and mevalonate diphosphate decarboxylase that is consistent with a peroxisomal localization of these enzymes. Finally, we show that cholesterol biosynthesis from mevalonate can occur in selectively permeabilized cells lacking cytosolic components. These results suggest that the peroxisome is the major site of the synthesis of FPP from mevalonate, since all of the cholestrogenic enzymes involved in this conversion are localized in the peroxisome.Recently, it has been demonstrated by our group and others that peroxisomes contain a number of enzymes involved in cholesterol biosynthesis that previously were considered to be cytosolic or located exclusively in the endoplasmic reticulum. Peroxisomes have been shown to contain acetoacetyl-CoA thiolase (1, 2), 3-hydroxy-3-methylglutaryl coenzyme A (HMGCoA) 1 synthase (3), HMG-CoA reductase (4 -6), mevalonate kinase (7,8), and most recently farnesyl diphosphate (FPP) synthase (9). Both mevalonate kinase and FPP synthase seem to be localized predominantly, if not exclusively, to peroxisomes (8, 9).The demonstration that mevalonate kinase and FPP synthase are localized predominantly in peroxisomes (8, 9) raises the question regarding the localization of the enzymes that catalyze the individual steps in the pathway between mevalonate kinase and FPP synthase (phosphomevalonate kinase, mevalonate diphosphate decarboxylase, and isopentenyl diphosphate isomerase). Based on results obtained from fractionation studies, these enzymes are believed to be localized in the cytosol. However, recent data have shown that the activities of these enzymes as well as mevalonate kinase and FPP synthase are significantly reduced in liver tissue obtained from patients with peroxisome-deficient diseases (Zellweger syndrome and neonatal adrenoleukodystrophy), thus indicating a peroxisomal localization (9).We have routinely employed three different methods to study subcellular localization of proteins: (i) analytical subcellular fractionation and measurements of enzyme activities, (ii) immunoblotting of the protein in the isolated fractions with a monospecific antibody, and (iii) immunoelectron and immunofluorescence micro...