The Mediterranean area is distinguished from most of the other parts of Europe in occurrence of many unique endemic fish species (especially cyprinids). Evidence and studies focussing on extensive research of parasitofauna of endemic freshwater fishes are rather exceptional. In the present study, we analysed the metazoan parasite communities in endemic cyprinid species of a large part of the Balkan Peninsula. A total of 577 specimens belonging to 57 cyprinid species were sampled in Albania, Bosnia and Herzegovina and Greece and examined for the presence of metazoan parasites. This study revealed over 100 species of metazoan parasites. The highest species diversity was reported within Monogenea, i.e. we reported 38 species of Dactylogyrus, from which 11 were identified as new, about 30 spp. of Gyrodactylus recognized on the basis of morphology (for confirmation of new species, molecular analysis is currently in progress), and Paradiplozoon homoion. Concerning Trematoda, 9 intestinal species – 7 species of Digenea in adult form (Allocreadium isoporum, A. markewitschi, Asymphylodora demeli, Sphaerostomum globiporum, Nicolla skrjabini, Plagioporus stefanski, Palaeorchis sp.), Aspidogaster cf. limacoides (Aspidogastrea) and Clinostomum sp. represented as metacercariae were found. In addition, Diplostomum spathaceum in the eye lens, and Tylodelphys clavata and Posthodiplostomum cf. brevicaudatum in eye vitreous humour were recorded. The adult tapeworms (Cestoda) Caryophyllaeus brachycollis, Proteocephalus torulosus and Schyzocotyle acheilognathi and larvae of Paradilepis scolecina and Proteocephalidae gen. sp. were found. Four adult nematode species, Rhabdochona hellichi, R. denudata, Schulmanella petruschewski and Hysterothylacium cf. fabri, and larvae of 6 species (Raphidascaris acus, Anguillicoloides crassus, Cosmocephalus obvelatus, Spiroxys sp., Contracaecum sp., Pseudocapillaria sp.) were recognized. Two species of Acanthocephala (Pomphorhynchus laevis and Acanthocephalus sp.) were recorded in intestine. From other ectoparasitic groups, 5 species of copepods of the genera Ergasilus, Neoergasilus, Paraergasilus and Lamproglena, Argulus sp. (Branchiura) and Hydrozetes cf. lemnae (Acari) (this last one is possibly an accidental presence of non-parasitic species or the species exploiting facultative strategy of parasitism), were reported. While the majority of species of Dactylogyrus and Gyrodactylus are characterised by a high degree of host specificity and include taxa endemic to the Mediterranean area, some monogeneans reported in endemic cyprinid species are commonly distributed in Europe. The remaining ectoparasites and all endoparasites are common parasites of cyprinids widely distributed in Palaearctic Region. We concluded that species diversity of parasites and their distribution in endemic cyprinid hosts are influenced by cyprinid biogeographical history (especially concerning the monogeneans), range of distribution of fish hosts and other abiotic and biotic factors. The study of parasite diversity in endemic cyprinids of the Balkan Peninsula (especially parasites exhibiting high host specificity) may represent a helpful tool for analysing biogeographical scenarios proposed for the historical distribution of Mediterranean cyprinids.