The miRNA pathway, as a fundamental mechanism of gene regulation, plays a key role in controlling the establishment, self-renewal, and differentiation of stem cells. Such regulation is manifested as fine-tuning the temporal- and tissue-specificity of gene expression. This fine-tuning function is achieved by (1) miRNAs form positive and negative feedback loops with transcription factors and epigenetic factors to exert concerted control of given biological processes; and/or (2) different miRNAs converge to control one or more mRNA targets in a signaling pathway. These regulatory mechanisms are found in embryonic stem cells, iPS cells, and adult tissue stem cells. The distinct expression profiles of miRNAs and their regulatory roles in various types of stem cells render these RNAs potentially effective tools for clinical diagnosis and therapy.