We have developed a combined micro-channel and micro-well system for easy cell loading, culture and post-culture operation on a chip. To demonstrate the reliability of the system, on chip cell culture and differentiation were performed with different types of substrates made of culture dish, glass cover slide and polydimethylsiloaxe (PDMS). As expected, mouse embryo fibroblasts (MEF) showed different adhesion and growth rate on different substrates. When embryonic stem (ES) cells were co-cultured with MEFs, the formation of ES colonies is efficient on both glass and Petri dish, although PDMS could also be used. Finally, ES cell differentiation with neuron growth factors was performed on different substrates, showing clear advantages of using culture Petri dish over both glass and PDMS.