The development of deep sequencing has enabled the identification of novel microRNAs (miRNAs), leading to a growing appreciation for the fact that individual miRNAs can be heterogeneous in length and/or sequence. These variants, termed isomiRs, can be expressed in a cell-specific manner, and numerous recent studies suggest that at least some isomiRs may affect target selection, miRNA stability, or loading into the RNA-induced silencing complex (RISC). Reports indicating differential functionality for isomiRs are currently confined to several specific variants, and although isomiRs are common, their broader biological significance is yet to be fully resolved. Here we review the growing body of evidence suggesting that isomiRs have functional differences, of which at least some appear biologically relevant, and caution researchers to take miRNA isoforms into consideration in their experiments.