© The Author 2017. Published by Oxford University Press for the Infectious Diseases Society of America. All rights reserved. Chlamydia trachomatis (Ct) infection causes significant morbidity. In vitro studies demonstrate that Ct growth inhibition occurs by interferon-gamma (IFN-γ 3)-mediated depletion of intracellular tryptophan, and some Ct strains utilize extracellular indole to restore tryptophan levels. Whether tryptophan levels are associated with Ct infection clearance in humans remains unknown. We evaluated tryptophan, indole, and IFN-γ 3 levels in cervicovaginal lavages from women with either naturally cleared or persisting Ct infection. Women who cleared infection had significantly lower tryptophan levels and trended toward lower IFN-γ 3 levels compared to women with persisting infection. Due to its volatility, indole was not measurable in either group.