Although roots are so important for plant growth and crop productivity, the molecular mechanism(s) of root formation and growth is not fully understood. To increase our understanding of the underlying molecular mechanisms, here we review microRNA regulation of processes related to root formation: the regulation of transcription factors, nutrient uptake, stress signaling, and growth signaling. We have summarized the interaction, expression, transport, and signaling events that involve microRNAs in ideal and stressed conditions in a number of model plants, highlighting the involvement of microRNAs in root formation. MicroRNAs are now known to be important players in root initiation, development, and growth; understanding the precise mechanisms involved will be valuable for plant molecular breeding to develop high-yielding crops with high stress resistance and low nutrient requirements.