To date, over 100 complete metazoan mitochondrial (mt) genomes of different phyla have been reported. Here, we briefly summarise mt gene organisation in the Metazoa and review what is known of the mt genomes of nematodes and flatworms parasitic in humans. The availability of complete or almost complete mtDNA sequences for several parasitic helminths provides a rich source of genetic markers for phylogenetic analysis and study of genetic variability in helminth groups. Examples of the application of mtDNA in studies on Ascaris, Onchocerca, Schistosoma, Fasciola, Paragonimus, Echinostoma, Echinococcus and Taenia are described.