The effectiveness of syndromic treatment as an STD control strategy depends on the proportion of episodes which become symptomatic; few studies have measured this directly. We estimated these proportions for gonorrhoea (NG) and chlamydia (CT), synthesizing data on the point prevalence of self-reported discharge and dysuria among infected cases in rural Uganda, the durations of symptoms, incubation period and asymptomatic episodes, and the effect of treatment on symptom duration. Estimated proportions of episodes that become symptomatic were 45% for males with NG, 11% for males with CT, 14% for females with NG and 6% for females with CT. This was on average 1.5-fold higher than symptom prevalence at cross-section among infected cases in this population. Estimates were sensitive to assumptions on the relative durations of asymptomatic and symptomatic episodes, but were invariably inconsistent with previous direct estimates based on a US cohort study. These results show that the probability of recognizing symptoms in NG and CT episodes varies between settings. In populations with low treatment rates like Uganda, these probabilities can be very low. Here, health education should have priority in STD management programmes.