An extensive and increasing number of mitochondrial genomes from a wide variety of different organisms have been sequenced but only limited information on the mitochondrial molecules of parasitic flatworms (Phylum Platyhelminthes: Classes Trematoda and Cestoda) has been available. Here we briefly summarise mitochondrial gene organisation in the Metazoa and then review new data on the mitochondrial genomes of several species of parasitic flatworms including Fasciola hepatica, Schistosoma spp., Paragonimus westermani and Echinococcus spp. which are of medical and/or veterinary importance. The availability of these complete or almost complete mitochondrial sequences provides an extremely rich and valuable source of genetic markers for phylogenetic analysis and study of genetic variability in the parasitic flatworms. The data will also facilitate studies on the processes of evolution influencing the mitochondrial genomes and genes themselves, and may provide new insights into mitochondrial function in parasitic flatworms leading to, for example, the identification of more effective drug targets.