RNA interference (RNAi) is widely used in high-throughput reverse genetics screens for basic research and drug discovery. However, this technique is known to produce “off-target” effects, or phenotypic results caused by an RNAi reagent’s knockdown of unintended genes rather than the gene of interest. Off-target effects are regulated through multiple mechanisms within the cell, and their presence can greatly complicate the interpretation of experimental data. We review the biology of offtargeting and discuss both bioinformatics and experimental approaches to reduce RNAi reagents’ off-target effects. Since such techniques cannot completely eliminate offtarget effects, we also discuss analysis methods developed to identify off-target effects in RNAi screening data and, in some cases, even leverage them to uncover novel biological functionality.