To compare the incidence of conjunctival infection with Chlamydia trachomatis in sexual partners of patients with newly diagnosed adult inclusion conjunctivitis (AIC) and a control group with healthy eyes. We also compare the observed signs and symptoms of conjunctival infection in patients with newly diagnosed AIC and their sexual partners. We performed a prospective comparative case-control study between patients with newly diagnosed AIC confirmed with direct fluorescent antibody (DFA) (n = 11), their sexual partners (n = 11), and a control group of healthy subjects (n = 11). Clinical history, physical examination, and a DFA test for C. trachomatis of a conjunctival scrapping from the tarsal conjunctiva were performed in all patients. A significantly higher frequency of positive DFA tests for C. trachomatis was observed in the sexual partner group (n = 8, 73 %) compared with the healthy control group (n = 2, 18.2 %) (P = 0.03). Ocular symptoms and signs were observed significantly more often in patients from the confirmed clinically active AIC group (n = 11, 100 %) than in their sexual partners (n = 2, 12.5 %). Sexual partners of patients with AIC are at greater risk of having an asymptomatic conjunctival infection with C. trachomatis than healthy subjects. Sexual partners might be considered a bacterial reservoir and a possible source for chlamydia reinfection. Not treating sexual partners might increase the probability of reinfection. More extended studies with a greater sample size should be done.