Wildlife populations represent an important reservoir for emerging pathogens and trans-boundary livestock diseases. However, detailed information relating to the occurrence of endemic pathogens such as those of the order Chlamydiales in such populations is lacking. During the hunting season of 2008, 863 samples (including blood, conjunctival swabs, internal organs and faeces) were collected in the Eastern Swiss Alps from 99 free-living red deer (Cervus elaphus) and 64 free-living roe deer (Capreolus capreolus) and tested using ELISA, PCR and immunohistochemistry for members of the family Chlamydiaceae and the genus Parachlamydia. Parachlamydia spp. were detected in the conjunctival swabs, faeces and internal organs of both species of deer (2.4% positive, with a further 29.5% inconclusive). The very low occurrence of Chlamydiaceae (2.5%) was in line with serological data (0.7% seroprevalence for Chlamydia abortus). Further investigations are required to elucidate the zoonotic potential, pathogenicity, and distribution of Parachlamydia spp. in wild ruminants.