The current understanding of metazoan relationships is largely based on analyses of 18S ribosomal RNA ('18S rRNA'). In this paper, DNA sequence data from 2 segments of 28S rRNA, cytochrome c oxidase subunit I, histone H3, and U2 small nuclear (sn)RNA were compiled and used to test phylogenetic relationships among the Mollusca, Annelida, and Arthropoda. The 18S rRNA data were included in the compilations for comparison. The analyses were especially directed at testing the implication of the Eutrochozoan hypothesis that the Annelida and Mollusca are more closely related than are the Annelida and Arthropoda and at determining whether, in contrast to analyses using only 18S rRNA, the addition of data from other genes would reveal these phyla to be monophyletic. New data and available sequences were compiled for up to 49 molluscs, 33 annelids, 22 arthropods, and 27 taxa from 15 other metazoan phyla. The Porifera, Ctenophora, and Cnidaria were used as the outgroup. The Annelida, Mollusca, Entoprocta, Phoronida, Nemertea, Brachiopoda, and Sipuncula (i.e., all studied Lophotrochozoa except for the Bryozoa) formed a monophyletic clade with maximum likelihood bootstrap support of 81% and a Bayesian posterior probability of 0.66 when all data were analyzed. The clade was also formed (including 1 arthropod, a symphylan) when only genes other than 18S rRNA were analyzed. Two molluscan genera with long branch lengths (Nautilus and Philippia) were removed from the Lophotrochozoa in the maximum-parsimony analyses of all data. The Ecdysozoa (comprised of the Kinorhyncha, Priapula, Nematoda, Onychophora, Tardigrada, and Arthropoda) was included in a clade with the Chaetognatha (with maximum-likelihood support of 80% and a Bayesian probability of 0.57) using the total data. This clade except the symphylan had a Bayesian probability of 0.66 when 18S r DNA data were excluded. The reciprocal separation of the Annelida and Mollusca was generally supported where this could be resolved. The monophyly of the Annelida was contradicted only by the inclusion of the Sipuncula and Brachiopoda and the exclusion of Owenia. Molluscan monophyly was contradicted by the anomalous placement of Nautilus and/or Philippia, but these taxa were never placed in the Annelida.