Chlamydiae cause a wide range of diseases in human and animal hosts. Chlamydia pneumoniae and Chlamydia trachomatis are important human pathogens with worldwide distribution that produce significant morbidity. Acute infections with C. pneumoniae cause respiratory tract infections, while chronic infection has been linked to chronic bronchitis, asthma and atherosclerosis. Ocular serovars of C. trachomatis induce trachoma, the leading cause of infectious blindness worldwide. C. trachomatis is the most common bacterial cause of sexually transmitted diseases (STDs) worldwide. Acute infections with genital serovars of C. trachomatis remain clinically silent in most women, but can progress to upper genital tract infection leading to pelvic inflammatory disease (PID), infertility and ectopic pregnancy. Chlamydia-induced, reactive arthritis can develop as a late-term condition after genital C. trachomatis or respiratory C. pneumoniae infection. In this review, we address recent information on pathogenesis, immune response, diagnosis and treatment of chronic diseases induced by C. trachomatis and C. pneumoniae.