C. trachomatis infects epithelial cells in the eye and genital tract. The early stage of infection can present itself through the emission or secretion of fluid containing mucus and pus from the eye, nose, cervix, vagina or other part of the body due to infection and inflammation. But infections are often in the process of producing or showing no symptoms at this stage. In utmost infected women the infection resolves, but in those with persistent or repeated infections, the infection can spread upwards from the endocervix to the fallopian tubes. Persistent infection eventually leads to fibrosis and scarring. In the eye, this leads to distortion of the eyelid margin, affecting the lashes and allowing them to turn inwards and rub against the cornea, a disease known as trachoma, which is a prominent cause of preventable blindness. In the same way, genital chlamydial infections can cause scarring of the fallopian tubes, leading to infertility or ectopic pregnancy as a result of tubal occlusion by scar tissue. With the exception of the lymphogranuloma venereum (LGV) strains, which cause systemic illness and infect regional lymph nodes, C. trachomatis infection usually remains confined to mucosal surfaces.

The EB travels from an infected person to the lungs of an uninfected person in small droplets and is responsible for infection. Once in the lungs, the EB is taken up by cells in a pouch called an endosome by a process called phagocytosis. However, the EB is not destroyed by fusion with lysosomes, as is typical for phagocytosed material. Instead, it transforms into a reticulate body (RB) and begins to replicate within the endosome. The reticulate bodies must use some of the host's cellular metabolism to complete its replication. The reticulate bodies then convert back to elementary bodies and are released back into the lung, often after causing the death of the host cell. The EBs are thereafter able to infect new cells, either in the same organism or in a new host. Thus, the lifecycle of C. pneumoniae is divided between the elementary body, which is able to infect new hosts but cannot replicate, and the reticulate body, which replicates but is not able to cause new infection.

The EB travels from an infected bird to the lungs of an uninfected bird or person in small droplets, and is responsible for infection. Once in the lungs, the EB is taken up by cells in a pouch called an endosome by a process called phagocytosis. However, the EB is not destroyed by fusion with lysosomes, as is typical for phagocytosed material. Instead, it transforms into a reticulate body and begins to replicate within the endosome. The reticulate bodies must use some of the host's cellular machinery to complete its replication. The reticulate bodies then convert back to elementary bodies, and are released back into the lung, often after causing the death of the host cell. The EBs are thereafter able to infect new cells, either in the same organism or in a new host. Thus, the life cycle of C. psittaci is divided between the elementary body which is able to infect new hosts, but can not replicate, and the reticulate body, which replicates, but is not able to cause new infection.