We described a protocol for dissecting the function of an important serine/threonine protein kinase, mammalian target of rapamycin (mTOR), in regulating the long-term undifferentiated growth of human embryonic stem cells (hESCs). The function of mTOR in hESCs was inactivated with a highly specific chemical inhibitor, rapamycin, and gene-specific small-hairpin RNAs, and the effects were evaluated under self-renewal or early differentiation conditions. We found that inactivation of mTOR impairs proliferation and enhances mesoderm and endoderm activities of hESCs. This protocol described a general strategy for studying the function of key genes and signaling events during hESC long-term self-renewal and early lineage specifications with pharmacological and genetic approaches.