Many studies have described surface markers of hematopoietic stem cells (HSCs) and mesenchymal stem cells (MSCs). However they are not generally regarded as specific markers and little is known about their expression profile during the culture of stem cells from the mononuclear cells (MNCs). This study investigated expression patterns of known adult stem cells markers in the bone marrow (BM) and peripheral blood (PB) MNCs in rats, and during the primary culture of BM MNCs at 6 days, 12 days, passage 1 and passage 2 by flow cytometry. The markers used were CD29, CD44 and CD90/Thy-1 for MSCs and CD34 and CD45 for HSCs, respectively. The results of the study showed that 1) the expression patterns of the surface markers were quite different between the fresh BM MNCs and passaged MSCs showing diverse patterns during the culture period, and 2) the surface markers of MSCs showed quite different expression patterns between the BM and PB MNCs, while those of HSCs showed almost same patterns between them. In more detail, CD29 appeared to be mainly expressed in adherent cells, while CD45 appeared to be mainly in floating cells. CD44 and CD90/Thy-1 were clearly expressed both in floating and adherent cells, although CD90/Thy-1 showed different intensities between two cell types. CD34 was not expressed significantly in all time points examined and its importance as a HSCs marker should be addressed further. These results suggest that many of the known surface markers of MSCs and HSCs might not represent stem cell populations in MNCs and hardly serve as true specific markers of stem cells.