Rodents are an important part of agricultural ecosystems, including within commercial orchards. In 2018–2020, we studied small mammals in commercial orchards in Lithuania (northern Europe), snap-trapping them twice a year (in June–July and September–October, 1450 individuals, 11 species) at 18 sites across central, northern, eastern, southern and western parts of the country. Sites were located in apple and plum orchards, as well as currant, raspberry and highbush blueberry plantations, with each site also having a control habitat (meadow or forest) adjacent. We present results of our analysis of body condition, based on body weight and body length in relation to the habitat type and the intensity of agricultural activities, and reproduction parameters (litter size, pregnancy disruption) in common, bank, short-tailed and root voles as well as yellow-necked and striped field mice, accounting for over 96% of trapped rodents. The average body condition index of A. flavicollis was C = 3.39, that of A. agrarius was C = 3.38, and of M. agrestis, M. arvalis, M. glareolus and M. oeconomus C = 3.29, 3.25, 3.23, and 3.01, respectively. Body condition of rodents was significantly dependent on species (p < 0.0001), age (p < 0.005) and gender (p < 0.05) of the individual, season (p < 0.0001) and habitat (p < 0.05); influence of crop age (p = 0.07) and intensity of agricultural practices (p = 0.12) was much weaker or insignificant. We found observed litter size decreasing in autumn in all rodents; that in M. arvalis and A. flavicollis was significant, and there was a tendency to decrease in M. oeconomus. A decrease of the observed litter size in area with higher intensity of agricultural practices was registered for M. arvalis and M. oeconomus, trend in M. glareolus was not significant. In A. flavicollis litter size was similar irrespective of intensity of agricultural practices. In spring, litter size was significantly correlated with the female body mass in M. oeconomus (r = 0.67, p < 0.05, body mass explained 45% of variation of the litter size) and A. flavicollis (r = 0.53, p < 0.005, 27% of litter size variation explained). In autumn, litter size and female body mass was positively correlated in all rodent species. Female body condition index and litter size correlations were weak. Therefore, old orchards with low intensity of agricultural practices are important habitats, maintaining sustainable rodent populations and diversity of animals in the agrolandscape.