The transcriptome is a key determinant of the phenotype of a cell and regulates the identity and fate of individual cells. Much of what we know about the structure and function of the transcriptome comes from studies averaging measurements over large populations of cells, many of which are functionally heterogeneous. Such studies conceal the variability between cells and so prevent us from determining the nature of heterogeneity at the molecular level as a basis for understanding biological complexity. Cell-to-cell differences in any tissue or cell culture are an essential feature of their biological state and function. This talk will cover recent work from my lab in generating and analyzing ultra high-throughput single cell RNA sequence data from cell cultures, and both solid and circulating human tissues. I will discuss some of the technical and computational challenges, and highlight possibilities for the rapid clinical utility of single cell sequencing technology.