Current national and international strategies for the control of Chlamydia trachomatis (CT) critically fail to obtain a reduction in transmission. In women, anorectal infections are about as common as genital CT. Yet anorectal CT remain untested as sexually transmitted infection (STI) clinics, general practitioners, hospital and population testing initiatives largely focus on genital CT. Part of untested anorectal CT is incidentally treated with the treatments applied for genital CT, as in women anorectal CT is often concurrent with genital CT. Yet, it is unknown whether transmission of anorectal CT can still occur after currently recommended treatment. Anorectal and genital CT were observed quite often after regular treatment (up to 40% detection by nucleic acid amplification tests-NAAT). Proposed reasons for such detection include a new (re-)infection from a partner or self-infection from another anatomic, e.g. anorectal, site. Anorectal infections are a potential reservoir for ongoing transmission of genital and anorectal CT in the population, between partners and between anatomic sites of an individual. Yet, neither the transmission potential nor the transmission impact of anorectal infections has been reported. The scientific evidence for the optimal control strategy for anorectal CT and thereby CT in its totality, is lacking.