Protein-coding genes with multiple alternative polyadenylation sites can generate mRNA 3UTR sequences of different lengths, thereby causing the loss or gain of regulatory elements, which can affect stability, localization and translation efficiency. 3USS is a web-server developed with the aim of giving experimentalists the possibility to automatically identify alternative 3 : UTRs (shorter or longer with respect to a reference transcriptome), an option that is not available in standard RNA-seq data analysis procedures. The tool reports as putative novel the 3 : UTRs not annotated in available databases. Furthermore, if data from two related samples are uploaded, common and specific alternative 3 : UTRs are identified and reported by the server.