Stem cells (SCs) are defined by their combined abilities to both self-renew indefinitely in vitro and differentiate into adult cell types. One of the major driving forces of SC research is that SCs may provide a potentially unlimited source for cell-replacement therapies in regenerative medicine. However, the identification of SCs and their progenies at different stages, and the success of cell-replacement therapies, which form the basis of SC engineering, will depend on the ability to characterize and ultimately isolate homogeneous primary stem or progenitor cell populations to a large degree. Furthermore, the recent identification of cancer stem cells (CSCs) opens a new avenue for developing novel therapeutic strategies by targeting a specific subset of cancer cells with self-renewal and proliferation capacity. Crucial to these tasks will be the discovery of novel plasma membrane-associated SC markers. In this review, we focus on the seminal contribution that membrane proteomics could make to further clinical applications of SCs by providing tools for purification and identification of SCs and their progenies at each stage of differentiation, as well as, to understand the underlying mechanisms of SC differentiation. The need to standardize biological SC models before embarking on international SC proteomics efforts is discussed.