Herein we report that an epistatic effect of the apoptosome components apaf-1 and caspase-9 on chlamydial infection and its host apoptosis regulation; that is, caspase-9 functions as in the sequestration model of pro-apoptotic factors for the regulation of host apoptosis, and Apaf-1 restricts chlamydial infection. Here, APAF1 is linked to chlamydia trachomatis infectious disease.