Blood parasites of Apodemus agrarius were investigated in Eastern Slovakia during 1998–2005. The following parasitic species were detected: Trypanosoma grosi, Babesia microti-like piroplasms and Bartonella sp. Trypanosoma grosi was the most common species, with an infection prevalence of 12.7%. Trypanosomes were morphologically typical of the lewisi group, however, they were bigger than T. grosi described in A. flavicollis and A. sylvaticus. The differences analysed by nested analysis of variance were statistically significant. Pleomorphism was not observed. Infections with piroplasms were detected only at two sites, with an intensity of infection not exceeding 0.1%. The morphology of the piroplasms was different from those typical of B. microti. Bartonella occurred at two sites in 0.81% of the animals sampled. The prevalence of infection had a seasonal pattern throughout the study years. Trypanosomes occurred from July to November, with a peak in September, piroplasms occurred in May and June, and Bartonella sp. from May to July.