Abstract Motivation: Although small nucleolar RNAs form an important class of non-coding RNAs, no comprehensive annotation efforts have been undertaken, presumably because the task is complicated by both the large number of distinct small nucleolar RNA families and their relatively rapid pace of sequence evolution. Results: With snoStrip we present an automatic annotation pipeline developed specifically for comparative genomics of small nucleolar RNAs. It makes use of sequence conservation, canonical box motifs as well as secondary structure and predicts putative targets. Availability and implementation: The snoStrip web service and the download version is available at http://snostrip.bioinf.uni-leipzig.de/ Contact: sebastian@bioinf.uni-leipzig.de