Purpose of reviewChronic diseases are common and deadly. Stem cell therapies have received intense interest for the repopulation of damaged or diseased tissues. A detailed understanding of the similarities and differences between embryonic stem cells and somatic stem cells will enhance our understanding of mechanisms of tissue repair or cellular augmentation. In addition, emerging technologies will be useful in the definition of the molecular regulation of the respective stem cell populations.Recent findingsA number of postnatal tissues have a population of somatic stem cells, which function in the maintenance and repair of tissues. Using molecular technologies these somatic stem cell populations have been shown to be pluripotent when placed in a permissive environment. Recent studies have utilized emerging technologies to define a molecular signature of embryonic stem cells and selected somatic stem cell populations. These strategies will be useful for the definition of a molecular program that promotes a stem cell phenotype (i.e. stemness phenotype).SummaryRecent studies suggest that embryonic and somatic stem cell populations hold promise as sources for tissue engineering. The use of cell biological and molecular technologies will enhance our understanding of embryonic and somatic stem cell populations and their molecular regulatory events that promote multipotentiation.