Cancer stem cells (CSCs), also known as tumor-initiating cells (TICs), are cancer cells that possess capability of proliferation, differentiation, and self-renewal. It is widely believed that CSCs play critical role in the initiation, metastasis, and relapse of cancers, but the origin of CSCs remains unclear. Up to date, several hypotheses have been described, and cell fusion and horizontal gene transfer, which may occur during development and tissue repair process, are considered as important origins of CSCs. In addition, critical gene mutations in stem cells, progenitor cells or even differentiated cells may also contribute to the formation of CSCs, and cell microenvironment is critical to CSC self-renewal and differentiation. The ongoing efforts to identify the CSCs origins may shed more light on understanding of cancer initiation and progression, as well as the development of novel cancer therapies.