An extensive survey of helminth parasites in 1,316 freshwater fish representing 31 species from two aquatic ecosystems in southeastern Slovakia characterized by different level of environmental pollution was carried out. The helminth species diversity was compared between the Tisa River, heavily polluted with cyanides and heavy metals after a series of ecological disasters in 2000, and the less anthropogenically influenced Latorica River. A parasitological survey found 31 gastrointestinal helminths: Trematoda (11 species), Cestoda (14), Acanthocephala (3) and Nematoda (3). As many as 70 host-parasite combinations have been found. Twenty of them (28.6%) represent new host-parasite finding records for the territory of Slovakia. The component communities were species-poor in both rivers, with high dominance of one to three helminth species. Even though the fish communities were qualitatively similar (ICS = 81%) and the number of fish examined was approximately the same (676 and 640) in both localities, the helminth species richness and diversity of host-parasite combinations were two times lower in the more polluted Tisa River. The helminth communities were also much less abundant in the Tisa River. Based on the Czekanowski-Sørensen similarity index (ICS = 48.8%) and the Percentage similarity index (PI = 19.5%), the helminth communities were qualitatively and quantitatively different in the two rivers. The remarkable lack of species diversity in the Tisa River can be explained by the negative impact of residual contamination of the Tisa river bottom on certain freshwater invertebrates (bivalves and prosobranch mollusks, copepods and amphipods) which serve as obligatory intermediate hosts for the helminths. Four species, the aspidogastrean Aspidogaster limacoides Diesing, 1835, the acanthocephalan Pomphorhynchus tereticollis (Rudolphi, 1809) tapeworms Atractolytocestus huronensis Anthony, 1958 and Khawia sinensis Hsü, 1935 are recorded in Slovakia for the first time.