Multiple methods currently exist for the assessment of peroxisome proliferation, including gene expression, enzyme activity, immunolabeling coupled with image analysis, and electron microscopy. This study describes a novel flow cytometric method to efficiently quantify peroxisome proliferation in cells from frozen livers. Frozen livers from cynomolgus monkeys treated with ciprofibrate at doses of 0, 3, 30, 150, and 400 mg/kg/day for 15 days were mechanically disaggregated using an automated dispersion method. The resulting cell suspensions were labeled using an allophycocyanin (APC)-conjugated antibody directed against peroxisomal membrane protein 70 (PMP70). Statistically significant increases in mean fluorescence intensity were observed from animals dosed at 30, 150, and 400 mg/kg/day compared to control. Parallel comparisons using electron microscopy and immunofluorescence microscopy suggest that flow cytometry may be an alternative to electron microscopy in determinations of peroxisome proliferation. Flow cytometric analysis of freshly isolated hepatocytes and frozen liver from rats treated with fenofibrate at 200 mg/kg/day for 10 days showed the flow cytometric method could detect peroxisome proliferation in both species. The research described here demonstrates the feasibility of applying flow cytometry for the detection of peroxisome proliferation.