More than 100 morphological, anatomical and histological characters pertaining to the Nudibranchia are discussed in the course of a phylogenetic analysis. Based on our own investigations on anatomy, histology and published literature, the polarity of each character is assessed by comparing its expression with outgroups, chiefly the Pleurobranchoidea, but also with other opisthobranch taxa (Cephalaspidea, Anaspidea, Sacoglossa), and ultimately with the Pulmonata, Vetigastropoda and Caenogastropoda. By extracting 46 applicable characters expressed in 30 taxa, a phylogenetic analysis of the major groups of the Nudibranchia is performed by using the computer program PAUP. Nudipleura new taxon (containing the Pleurobranchoidea plus Nudibranchia) is defined. The monophyly of the Nudibranchia, the Anthobranchia (containing the Bathydoridoidea plus Doridoidea), and the Cladobranchia (containing the Dendronotoidea plus Aeolidoidea and ‘Arminoidea’) are confirmed and autapomorphies are highlighted. The paraphyly of the ‘Arminoidea’ is demonstrated. Incongruities at lower taxonomic level are discussed.