In this study, a new microfluidic system is presented which can culture and differentiate MSCs in situ. It is composed of several micro-components, including seeding reservoirs, culture areas, micropumps, microgates, waste reservoirs and fluid microchannels. All of them are fabricated by using micro-electro-mechanical-systems (MEMS) technology. The automated system allows for the long-term culture and differentiation of MSCs. Two methods, including Oil Red O staining for adipogenic cells, and alkaline phosphatase staining for osteogenic cells are used to assess the differentiation of MSCs. Experimental results clearly demonstrate that the MSCs can be cultured for proliferation and different types of differentiation are possible in this microfluidic system.