Embryonic and adult stem cell populations have great potential value in medicine, and hematopoietic stem cells are already being used in transplantation. Definition of these populations to increase our understanding of the programs that control differentiation, self-renewal, and possibly plasticity would be of great interest. The relative quantitation of transcriptional activity in stem cells and other populations has defined a profile of gene expression activity in stem cells. Confirmation that these differences have an impact on protein levels within stem cells via their complete protein complement and protein interactions will enable further understanding of regulatory processes in these cells. The recent developments in proteomics and their potential application to the definition of the stem cell proteome are discussed, and examples are given. Advances in mass spectrometry, subcellular prefractionation protocols, and electrophoresis that make stem cell proteomics a tractable problem are discussed. Beyond the proteome per se, advances in post-translational modification profiling mean that comparative analysis of phosphorylation patterns between stem cells and other populations can be approached.