Background. Untreated Chlamydia trachomatis infections in women can result in disease sequelae such as pelvic inflammatory disease (PID), ultimately culminating in tubal occlusion and infertility. While nucleic acid amplification tests can effectively diagnose uncomplicated lower genital tract infections, they are not suitable for diagnosing upper genital tract pathological sequelae. Objective. The purpose of this paper was to provide a comprehensive review of new molecular factors associated with the diagnosis and prognosis of PID. Material and Methods. The literature was searched using the key words "Chlamydia trachomatis infections," "pelvic inflammatory disease," and "molecular factors" in the PubMed database. Relevant articles published between 1996 and 2012 were evaluated. Conclusions. The use of new molecular factors could potentially facilitate earlier diagnosis and prognosis in women with PID due to C. trachomatis infection.