Flow cytometry (FCM) has become known as a useful tool for examining numerous cells in a micronucleus test in a short time. To successfully count micronuclei, immature erythrocytes and micronuclei need to be specifically stained and CD71-based FCM, with anti-CD71 antibody for immature erythrocytes and propidium iodide (PI) for micronuclei is a widely accepted tool. Because staining with fluorescent dyes may be much simpler compared to immunostaining, attempts are being made to develop a fluorescent dye-based FCM (FD-FCM). The aim of this study was to provide a practical FD-FCM method. Peripheral blood (PB) erythrocytes and bone marrow (BM) erythrocytes were obtained from rats treated with cyclophosphamide at a dose of 20mg/kg for two days. Nucleic cells of BM samples were eliminated using a cellulose column. Then erythrocytes were fixed, stained with Hoechst 33258 and PI and examined with FCM. Mean FD-FCM values of micronucleated immature erythrocytes in PB and BM were respectively 110% and 77% of the values obtained by microscopy. Percentages of mean immature erythrocyte values by FCM to those by microscopy were 74% and 94%. These data suggest that the simple method, composed of column purification of erythrocytes, methanol fixation, fluorescent dye staining and FCM, was useful for automated scoring in micronucleus testing of rat BM and PB.