Wildlife populations represent an important reservoir for emerging pathogens and transboundary livestock diseases. However, exact knowledge on common domestic pathogens such as Chlamydiales in these populations is lacking. During the hunting season of 2008, 863 samples, including blood, eye swabs, organs and fecal samples, from 99 red deer and 64 roe
deer were collected in the eastern Swiss Alps, and samples were tested by ELISA, PCR and immunohistochemistry for Chlamydiaceae and Parachlamydia. Parachlamydia was detected
in eye swabs, fecal samples and organs of free-living deer (2.4% positives and 29.5% questionable positives). The very low occurrence of Chlamydiaceae (2.5%) was in agreement with the few positive serological results (0.7% seroprevalence for C. abortus). Further investigations on Parachlamydia are needed to elucidate the zoonotic potential, the pathogenicity, and distribution in wild ruminants.