Three cases of atypical pneumonia in individuals working at a poultry slaughterhouse prompted an epidemiological survey in 10 poultry farms that had supplied birds. Using a Chlamydiaceae-specific real-time PCR assay, chlamydial agents were detected in 14 of 25 investigated flocks. Rather unexpectedly, Chlamydophila psittaci was identified only in one of the positive flocks, whereas ArrayTube DNA microarray testing indicated the presence of a new, so far unclassified member of the genus Chlamydophila. For further characterization of the agent involved, positive cloacal swabs were used to inoculate embryonated chicken eggs and isolates were obtained from 6 different flocks. Sequencing of 16S rRNA genes revealed nearly identical sequences of all samples. Alignment with representative sequences of Chlamydiaceae showed the separate position of the present strains outside the currently recognized species of Chlamydophila, but clearly within this genus. In contrast, partial ompA gene sequences displayed considerable diversity among the isolates, which had already been observed in restriction enzyme analysis of ompA PCR products. These data suggest that each farm had been infected with a different strain of this new chlamydial agent, the zoonotic potential and the exact taxonomic status of which have yet to be defined.