To determine whether the initiation of highly active antiretroviral therapy (HAART) had any influence on the incidence of disseminated histoplasmosis, a retrospective cohort study was performed on 1551 patients followed for up to 12 years. After controlling for CD4 counts, age, and sex, patients taking HAART for 2 months or less were more likely to develop disseminated histoplasmosis than untreated patients (respectively, hazard ratio, 3.7 [95% confidence interval, 1.57-8.7]; P = 0.003). In contrast, after 6 months of HAART, treated patients were less likely to develop disseminated histoplasmosis than untreated patients (hazard ratio, 0.6 [95% confidence interval, 0.37-0.98], P = 0.04). This increased incidence suggests that the initiation of HAART and the subsequent immune reconstitution may reveal undiagnosed latent disseminated histoplasmosis.