It has since long been reported that Chlamydia psittaci is endemic in the poultry industry in Belgium as well as in other European Countries. This can lead to major economic losses because of a lowered egg production, higher mortality and carcass condemnation. Nowadays, expensive antibiotic treatments are necessary to reduce mortality rate but this can lead to antibiotic resistance. Moreover, C. psittaci can easily be transmitted from birds to humans through the inhalation of pathogen-containing aerosols derived from feces and eye and nostril secretions. Therefore, the need for an efficient vaccine against C. psittaci is augmenting. However, more research is needed to develop such a vaccine. Knowledge on the immune mechanisms of C. psittaci infections is crucial to understand the pathogenesis of, and immunity to this zoonotic pathogen and to act as a basis for vaccination studies. This study has investigated the in vivo immune response evoked by C. psittaci in his natural host, the chicken. Excretion of C. psittaci, chlamydial antibody detection in sera, blood immune cells and the mRNA expression levels of different cytokines, chemokines and one Toll-like receptor were investigated in different organs (conchae, lungs, airsacs, harderian gland, bursa fabricius and spleen) at different time points post infection (6h, 24h, 48h, 4d, 6d, 8d, 10d, 14d and 21d). A higher frequency of cytotoxic CD8+ T cells and monocytes/macrophages expressing the MHC II molecule were observed in the infected group. Several cytokines and chemokines are significantly upregulated during infection but remarkably also significantly downregulated, especially at late time points. Furthermore, the only Toll-like receptor investigated, TLR4, was also significant upregulated in several organs. This study can contribute on the elucidation on how C. psittaci interact with his host, leading to the developing of targets for effective vaccination and therapeutic strategies for infection.