Insight, innovation, integrationHeterogeneity of stem cell populations is a well-known but poorly characterized phenomenon. Here, we provide single-cell transcript profiles of individual human embryonic stem cells that clearly identify cellular heterogeneity in these populations and identify novel cell types. This transcript analysis is presented at a level of depth and resolution not attainable by other methods. None of the insights in this study would have been possible with standard population-level transcript analysis or single-cell FACS analysis of known cell surface markers. Only by developing robust single-cell transcript profiling techniques and applying these to established stem cell differentiation paradigms were we able to deconstruct complex populations of cells into their component parts.