Abstract Background Sequencing is the key method to study the impact of short RNAs, which include micro RNAs, tRNA-derived RNAs, and piwi-interacting RNA, among others. The first step to make use of these reads is to map them to a genome. Existing mapping tools have been developed for long RNAs in mind, and, so far, no tool has been conceived for short RNAs. However, short RNAs have several distinctive features which make them different from messenger RNAs: they are shorter, they are often redundant, they can be produced by duplicated loci , and they may be edited at their ends. Results In this work, we present a new tool, srnaMapper, that exhaustively maps these reads with all these features in mind, and is most efficient when applied to reads no longer than 50 base pairs. We show, on several datasets, that srnaMapper is very efficient considering computation time and edition error handling: it retrieves all the hits, with arbitrary number of errors, in time comparable with non-exhaustive tools.