To assess long-term effects of naturally occurring infection with Chlamydophila spp. on animal health, 25 calves were grouped according to their chlamydial carrier status and checked for health parameters from 2 to 7 months of age. Monthly PCR testing revealed persistent or frequently recurring infections with Chlamydophila pecorum and Chlamydophila abortus in Group 2 (Chl+, n=13), but not in Group 1 (Chl-, n=12). Despite the absence of any clinical illness, calves in Group 2 showed significantly higher body temperatures (subfebrile), lower bodyweights, reduced serum iron concentrations, lower total haemoglobin and haematocrit values. Counting and flow cytometric differentiation of peripheral white blood cells revealed a general decrease in leukocytes in Group 2. At necropsy, follicular bronchiolitis was found in 10/13 calves in Group 2 but in none of Group 1, and the weight of pharyngeal tonsils was significantly higher in Group 2. In conclusion, naturally occurring infections with Chlamydophila species in calves were found to be associated with chronic effects on animal health at a subclinical level.