MSA Class Logos is a free web server allowing users to group amino acid sequences into classes and generate sequence logos for each class as well as the entire multiple sequence alignment. The web server is intended to assist scientists with little or no programming skills. Input files are a multiple sequence alignment in FASTA format (required) and, optionally, a file specifying the class each sequence belongs to in CSV format. After file upload, one reference sequence needs to be selected. This sequence will be displayed separately for comparison in the Class Specific Logos tab. This can be any sequence from the multiple sequence alignment and is just for convenience in case it is interesting to compare a particular sequence to the sequence logos of each class. If this is not important, any sequence can be selected since it does not affect the generation of the logos and, therefore, the results displayed. There are two tabs with different results available. The first one shows the complete multiple sequence alignment with all sequences sorted according to the classes defined by the user and a sequence logo considering all sequences. This alignment and sequence logo are explorable directly on the web page. The second tab shows sequence logos separated for each defined class, which allows the identification of positions that are conserved in only a subset of sequences but not in all. In other words, the second view (tab) allows a more detailed analysis of a multiple sequence alignment that permits the identification of class-specific conserved residues in evolutionary and/or functionally variable protein groups. Results can be reviewed visually directly on the web page or downloaded as tables in CSV format. Additionally, sections of each sequence logo can be downloaded in SVG and used to generate figures for publications or presentations.