Chlamydia species invade the cell, and express proteins that form a protective inclusion membrane (chlamydia inclusion); and then act like a pathogen-specific parasitic organelle. Different chlamydia species express different types of proteins, to form the protective membrane. The pathogen is sheltered from the immune system by the cell wall and the protein-membrane encapsulating the pathogen, as it reproduces and spreads to new host cells.

Chlamydia lives inside the cell, with up to 42 million proteins, and can generate or cause abnormal proteins inside the cell, in the inclusion membrane, and outside the chlamydia inclusion. Chlamydia also infects immune cells, and infected immune cells spread the pathogen to other organ systems in the body.