Microbial cure of chlamydia proctitis (lymphogranuloma venereum [LGV] and non-LGV) with doxycycline treatment was evaluated by chlamydia DNA and RNA persistence in anal swab specimens. In LGV proctitis, RNA persisted for up to 16 days. In non-LGV chlamydia proctitis, DNA was undetectable after 7 days. These findings support the Centers for Disease Control and Prevention's treatment recommendation of a 21-day doxycycline regimen for LGV proctitis and a 7-day regimen for non-LGV chlamydia proctitis. Delayed microbial cure of LGV proctitis should be considered in improved treatment regimens.