Objective: Determine the impact of HIV-1 seroconversion on inflammatory cytokines in the rectal mucosa.Setting: Secondary analysis of data from men who have sex with men and transgender women who participated in a HIV prevention trial Lima, Peru.Methods: From July to December 2017, 605 men who have sex with men and transgender women were screened for rectal gonorrhea/chlamydia (GC/CT). Fifty GC/CT-positive cases were randomly selected and matched with 52 GC/CT-negative controls by age and number of receptive anal intercourse partners in the last month. All participants were HIV-negative at baseline and those with GC/CT at baseline and/or follow-up received appropriate antibiotic therapy. Participants underwent sponge collection of rectal secretions for the measurement of inflammatory cytokines (IL-1β, IL-6, IL-8, and TNF-α) and were screened for rectal GC/CT and HIV at baseline, 3 months, and 6 months. Wilcoxon rank-sum tests compared inflammatory cytokine levels between participants diagnosed with HIV during follow-up and persons who remained HIV-negative.Results: Eight participants were diagnosed with HIV at the 3-month (n = 6) or 6-month (n = 2) visit. The median number of receptive anal intercourse partners in the month before HIV diagnosis was the same for those who acquired HIV and those who did not. There were no significant differences in inflammatory cytokine levels in rectal mucosa between participants who did and did not experience HIV seroconversion at any time point.Conclusions: Despite a surge in viral replication during acute infection, findings from this study suggest that there is no prolonged effect of HIV-1 seroconversion on inflammatory cytokine levels in the rectal mucosa.