The protozoa kingdom comprises a large number of species, including some which are agents of human and veterinary diseases such as malaria, leishmaniasis, Chagas’ disease, African trypanosomiasis, amebiasis, trichomoniasis, giardiasis, toxoplasmosis, coccidiosis, theileriosis and babesiosis, to mention only the more important ones. Some of these protozoa, as is the case of Trichomonas, present a simple life cycle. For others, however, as occurs with Apicomplexa (which includes Plasmodium, Toxoplasma, Eimeria, etc) and some trypanosomatids, the life cycle is relatively complex, displaying several developmental stages in the vertebrate host and, in some cases, in invertebrate hosts. These protozoa are also of interest from the cell biology point of view since they present special cytoplasmic structures and organelles, which have been studied in some detail during the last few years providing new information of general biological interest. These studies have shown that new metabolic pathways take place in these organelles opening up possibilities to identify new drug-targets and new drugs for the treatment of patients and animals with diseases caused by protozoa. Here, I will briefly point out some introductory information on the cytoskeleton organization of pathogenic protozoa. Further information can be found in the various chapters which compose this special issue of Trends in Cell and Molecular Biology.