Prevalence and abundance of Bartonella spp. infections were studied over a 3-year period in woodland and grassland rodents in North-Eastern Poland. Prevalence of bacterial infections was similar in the two rodent communities, with one leading host species in each habitat (46·3% in Apodemus flavicollis versus 29·1% in Myodes glareolus in forest, or 36·9% in Microtus arvalis versus 13·7% in Mi. oeconomus in grassland). Prevalence/abundance of infections varied markedly across the 3 years with 2006 being the year of highest prevalence and abundance. Infections were more common during autumn months in My. glareolus and A. flavicollis, and in juvenile and young adult (age classes 1 and 2) My. glareolus and Mi. oeconomus than in adults (age class 3). Higher prevalence and abundance of Bartonella infections were found in male A. flavicollis in comparison to females. These data are discussed in relation to the parasite genotypes identified in this region and with respect to the role of various ecological factors influencing Bartonella spp. infections in naturally infected host populations.