The relationship between the body condition of different small mammal species and the habitat they occupy is poorly analyzed. We analyzed the body condition index, BCI, of 18 small mammal species trapped in forest, shrub, wetland, meadow, riparian, mixed and fragmented, disturbed, agricultural, and commensal habitats of Lithuania during the span of 1980–2023. The composition of small mammal communities was habitat-dependent, being richest in meadows, with eighteen species, and poorest in riparian habitats, with nine species. A significant variation in the BCI with respect to habitat was observed in eight small mammal species (Sorex araneus, S. minutus, Apodemus agrarius, A. flavicollis, Clethrionomys glareolus, Alexandromys oeconomus, Microtus agrestis, and M. arvalis). The highest average BCI for most of these species was found in disturbed habitats, with S. minutus and M. arvalis showing the highest BCI in agricultural habitats. The lowest average BCI for most species was found in mixed habitats, while C. glareolus and M. arvalis exhibited the lowest BCI in shrub habitats. In general, species dominating certain habitats did not have the highest BCI. This is the first multi-species, multi-habitat study of body condition in small mammals at mid-latitudes.