Chlamydial protease-like activity factor (CPAF) is secreted to the cytoplasm of the infected cells where it proteolytically cleaves eukaryotic transcription factor RFX5. Here, we determined the localization pattern of CPAF during the course of an acute and persistent in vitro infection of the epithelial cell line HEp-2 with Chlamydophila pneumoniae strain VR1310. Using immunoblotting, confocal microscopy and electron microscopy, we found CPAF in the inclusion lumen or associated with bacteria during the first 48 h of an acute infection. Seventy-two hours and later, CPAF was present predominantly in the cytoplasm of the infected cells. Translocation of CPAF into cytoplasm correlated in time with degradation of the transcription factor RFX5, as confirmed by immunoblotting. Interestingly, during the persistent infection induced by either IFN-gamma or iron limitation CPAF translocation to the cytoplasm was inhibited resulting in unaffected or only partially reduced levels of RFX5. Based on presented findings, we propose that CPAF translocation to the cytoplasm is separated from its production. The translocation mechanism appears to be fully active during an acute infection; however, it is fully or partially inhibited during persistent infection induced by IFN-gamma or by iron limitation respectively. Consequently, this work demonstrates the importance of subcellular localization of CPAF for the characteristics of chlamydial acute and persistent infection in epithelial HEp-2 cells.