The phylogenetic positions of Cycliophora and Micrognathozoa are examined in a computer-assisted cladistic analysis of Metazoa. In the preferred tree, Cycliophora and Entoprocta form a monophylum, supported by the presence of mushroom-shaped extensions into the epidermis, originating from the basal lamina. An earlier suggested close relationship between Cycliophora and Ectoprocta is rejected. The rotifer-like animal Micrognathozoa is placed in the clade Gnathifera, which also contains Gnathostomulida, Seisonida, Acanthocephala and Eurotatoria. Gnathifera is supported by the presence of jaws with a unique ultrastructure and cross-striated muscles attached to the jaw elements by epithelial cells. The jaws in Acanthocephala are considered secondarily reduced. In the analysis, Rotifera turns out to be paraphyletic with respect to Acanthocephala.