We present parsimony analyses of annelids based on the largest taxon sample and most extensive molecular data set yet assembled, with two nuclear ribosomal genes (18S rDNA and the D1 region of 28S rDNA), one nuclear protein coding-gene (Histone H3) and one mitochondrial ribosomal gene (16S rDNA) from 217 terminal taxa. Of these, 267 sequences are newly sequenced, and the remaining were obtained from GenBank. The included taxa are based on the criteria that the taxon must have 18S rDNA or at least two other loci. Our analyses show that 68% of annelid family ranked taxa represented by more than one taxon in our study are supported by a jackknife value > 50%. In spite of the size of our data set, the phylogenetic signal in the deepest part of the tree remains weak and the majority of the currently recognized major polychaete clades (except Amphinomida and Aphroditiformia) could not be recovered. Terbelliformia is monophyletic (with the exclusion of Pectinariidae, for which only 18S data were available), whereas members of taxa such as Phyllodocida, Cirratuliformia, Sabellida and Scolecida are scattered over the trees. Clitellata is monophyletic, although Dinophilidae should possibly be included, and Clitellata has a sister group within the polychaetes. One major problem is the current lack of knowledge on the closest relatives to annelids and the position of the annelid root. We suggest that the poor resolution in the basal parts of the trees presented here may be due to lack of signal connected to incomplete data sets both in terms of terminal and gene sampling, rapid radiation events and/or uneven evolutionary rates and long-branch attraction.