The immunomodulatory property of mesenchymal stem cells (MSCs) has been previously reported. Still it is unclear if this property can be affected by the cell origin and cell quality. Using primary MSCs expanded from bone marrow (BM-MSCs) and adipose tissue (AD-MSCs) of mice, we investigated whether the immunomodulatory property of MSCs varied with cell origin and cell quality (early- vs. late-passaged BM-MSCs). BM-MSCs (p1) and AD-MSCs (p1) had a typical spindle shape, but morphological changes were observed in late-passaged BM-MSCs (p6). A pathway-focused array showed that the expression of chemokine/cytokine genes varied with different cell origins and qualities. By co-culturing with spleen mononuclear cells (MNC) for 3 days, the expression of CD4 was suppressed by all types of MSCs. By contrast, the expression of CD8 was suppressed by BM-MSCs and increased by AD-MSCs. The expression ratio of CD206 to CD86 was at a comparable level after co-culture with AD-MSCs and BM-MSCs, but was lower with late-passaged BM-MSCs. AD-MSCs highly induced the release of IL6, IL-10 and TGF-β in culture medium. Compared with early-passaged BM-MSCs (p1), late-passaged BM-MSCs (p6) released less TGF-β. Our data suggests that the immunomodulatory properties of MSCs vary with cell origin and cell quality and that BM-MSCs of good quality are likely the optimal source of immunomodulation.