MicroRNAs are a class of endogenous non-coding RNAs that function as important regulatory molecules via the RNA interference mechanism. Since microRNAs play a fundamental role in regulation of a variety of cellular, physiological, and developmental processes, their aberrant expression can lead to a variety of human diseases including cancer. In particular, microRNAs have been implicated in regulation of stem cells as well as cancer stem cells. Given that cancer stem cells are believed to be responsible for the cancer initiation, metastasis and chemotherapy resistance, a better understanding of how microRNAs mediate gene expression in cancer stem cells will help identify novel cancer biomarkers and therapeutic targets, and as a result, it will aid in the development of better strategy for cancer treatment. In this review, we will update recent advances in microRNAs involved in cancer stem cells and their gene regulations in these cells.