MicroRNAs are short, approximately 22 nucleotide noncoding RNAs binding to partially complementary sites in the 3′UTR of target mRNAs. This process generally results in repression of multiple targets by a particular microRNA. There is substantial interest in methods designed to predict the microRNA targets and effect of single nucleotide polymorphisms (SNPs) on microRNA binding, given the impact of microRNA on posttranscriptional regulation and its potential relation to complex diseases. We developed a web‐based application, MicroSNiPer, which predicts the impact of a SNP on putative microRNA targets. This application interrogates the 3′‐untranslated region and predicts if a SNP within the target site will disrupt/eliminate or enhance/create a microRNA binding site. MicroSNiPer computes these sites and examines the effects of SNPs in real time. MicroSNiPer is a user‐friendly Web‐based tool. Its advantages include ease of use, flexibility, and straightforward graphical representation of the results. It is freely accessible at http://cbdb.nimh.nih.gov/microsniper. Hum Mutat 31:–11, 2010. © 2010 Wiley‐Liss, Inc.