Human embryonic stem cells (hESCs) offer exciting potential in regenerative medicine for the treatment of a host of diseases including cancer, Alzheimer's and Parkinson's disease. They also provide insight into human development and disease and can be used as models for drug discovery and toxicity analyses. The key properties of hESCs that make them so promising for medical use are that they have the ability to self-renew indefinitely in culture and they are pluripotent, which means that they can differentiate into any of more than 200 human cell types. Since proteins are the effectors of cellular processes, it is important to investigate hESC expression at the protein level as well as at the transcript level. In addition, post-translational modifications, such as phosphorylation, may influence the activity of pivotal proteins in hESCs, and this information can only be determined by studying the proteome. In this review, we summarize the results obtained from several proteomics analyses of hESCs that have been reported in the last few years.