MicroRNAs are short strands of RNA that regulate gene expression. Particular microRNAs each have unique expression domains, targets, and gain- and loss-of-function phenotypes that have important implications for directed differentiation of stem cell populations and suppression of undesired cell types. We discuss this emerging topic, in part using muscle differentiation as a paradigm, and highlight common themes and unique modalities by which microRNAs exert their lineage-promoting or differentiation effects on multiple tissues.