Flatworms (phylum Platyhelminthes) are favourite organisms in Developmental Biology and Zoology because of their extraordinary powers of regeneration and because they may hold a pivotal place in the origin and evolution of the Bilateria. Hox genes play key roles in both processes: setting up the new anteroposterior pattern in the former, and as qualitative markers of phylogenetic affinities among bilaterian phyla in the latter. We have searched for Hox and ParaHox genes in several flatworm groups spanning from freshwater triclads to marine polyclads and, more recently, in the acoels, the likely earliest extant bilaterian. We have isolated and sequenced eight Hox genes from the freshwater triclad Girardia tigrina and three Hox and two ParaHox genes from the polyclad Discocelis tigrina. Data from the acoels Paratomella rubra and Convoluta roscoffensis is also reported. Flatworm Hox sequences and 18S rDNA sequence data support clear affinities of Platyhelminthes to spiralian lophotrochozoans. The basal position of acoel flatworms supported from recent 18S rDNA data, remains still uncertain. Expression of Hox genes in intact and regenerating adult organisms show nested patterns with graded anterior expression boundaries, or ubiquitous expression. New approaches to study the function of Hox genes in flatworms, such as RNA interference are briefly discussed.