Lophotrochozoa has been consistently recovered in molecular phylogenetic analyses using different markers. Current knowledge of lophotrochozoan relationships is reviewed and the place that parasites occupy in this phylogeny is discussed. Two major taxa are identified within Lophotrochozoa: Platyzoa and Trochozoa. Monophyly of both taxa is still under debate. Relationships within Trochozoa remain largely unclear, however, there is strong evidence that the so called "minor phyla" Sipuncula, Echiura, and Myzostomida are all nested within annelids. Monophyly of the former "Lophophorata" is rejected, and a close relationship between phoronids and brachiopods, as well as between bryozoans and kamptozoans is suggested instead. The movement of the field of systematics into the genomic era will greatly improve our knowledge in the near future.