RBPmotif web server (http://www.rnamotif.org) implements tools to identify binding preferences of RNA-binding proteins (RBPs). Given a set of sequences that are known to be bound and unbound by the RBP of interest, RBPmotif provides two types of analysis: (i)de novomotif finding when there is no a priori knowledge on RBP’s binding preferences and (ii) analysis of structure preferences when there is a previously identified sequence motif for the RBP.De novomotif finding is performed with the previously published RNAcontext algorithm that learns discriminative motif models to identify both sequence and structure preferences. The results of this analysis include the inferred binding preferences of the RBP and the added predictive value of incorporating structure preferences. Second type of analysis investigates whether the instances of the previously identified sequence motif are enriched in a particular structure context in bound sequences, relative to its instances in unbound sequences. On completion, the results page shows the comparison of structure contexts of the motif instances between bound and unbound sequences and an assessment of statistical significance of detected preferences. In summary, RBPmotif web server enables the concurrent analysis of sequence and structure preferences of RBPs through a user-friendly interface.