The helminths of two sympatric species of rodents, the striped field mouse Apodemus agrarius and the yellow-necked mouse, Apodemus flavicollis from Slovakia were studied to determine whether there are similarities in the composition of the helminth fauna of two closely related host species living in the same area. A total of twelve species of helminths were identified in these rodent populations, including Brachylaima sp. (Trematoda); Hymenolepis diminuta (Rudolphi, 1819), Mesocestoides sp. larvae, Rodentolepis fraterna (Stiles, 1906), Rodentolepis straminea (Goeze, 1782), Skrjabinotaenia lobata (Baer, 1925), Taenia taeniaeformis larvae (Batsch, 1786) (Cestoda); Aonchotheca annulosa (Dujardin, 1845), Heligmosomoides polygyrus (Dujardin, 1845), Heterakis spumosa Schneider, 1866, Mastophorus muris (Gmelin, 1790) and Syphacia stroma (Linstow, 1884) (Nematoda). In A. agrarius, H. polygyrus was the most prevalent, as well as the most abundant helminth, but R. fraterna was the species with the highest mean intensity. In contrast, S. stroma dominated the A. flavicollis helminth fauna with the highest prevalence, mean abundance and mean intensity. Both rodent populations harboured nine helminth species, although the mean individual species richness was significantly higher in A. agrarius than in A. flavicollis. The analysis of helminth diversity at both component and infracommunity levels revealed differences between the two rodent populations, which are most likely attributable to the specific host ecology.