The application of biochemical and molecular techniques in parasitological studies has provided increasing evidences of genetic polymorphism among parasite populations. This review presents possible origins of genetic variation within populations of various protozoan species. Since the mode of reproduction has an important influence on genetic polymorphism within parasite populations these considerations refer mainly to some protozoan parasites which have various life cycles, e.g. Giardia, Trypanosoma, Cryptosporidium, Toxoplasma. Also other factors associated with parasites (such as: transmission and passage history in laboratory conditions; occurrence in different hosts or geographic regions; selective pressure of drugs; competitive interactions between populations) that affect parasite genetic diversity are discussed. However, the number of examined isolates of parasites and genetic markers, assortment of methods, probes, primers and reagents used is also of significance. The significance of genetic variability in parasite populations is still the subject of much interest and controversy. A simple interpretation of such variation is impossible because of the complexity of host-parasite interactions. The knowledge of parasite diversity at the nucleic acids level has continually increased, but a corect interpretation of this phenomenon requires at least the same knowledge of genetic variability in host populations. Nevertheless, genetic variability in protozoan parasites has many important implications, e.g. for taxonomy, epidemiology, control and evolution. Genetic differences within parasite populations might also be associated with phenotypic variability, e.g. virulence, antigenicity, infectivity, drug sensitivity, host preference etc.