We compared changes in the relative frequencies of opportunistic illnesses (OIs) among 1,044 Taiwanese persons with HIV infection who were enrolled in three study periods from June 1994 to June 2004: before the introduction of highly active antiretroviral therapy (HAART); early HAART; and late HAART. Nearly two-thirds of those newly diagnosed with HIV infection had CD4 counts below 200/mm(3). Among a total of 1, 182 OIs, candidiasis, Pneumocystis carinii pneumonia, and tuberculosis were the most common in all three study periods within 3 months after enrollment. Within 3 to 12 months after enrollment, the number of OIs declined significantly. Only 81 cases of OIs were diagnosed, the most common of which were cytomegalovirus disease, tuberculosis, candidiasis, and Mycobacterium avium complex infection. Except for the decreasing frequency of Kaposi's sarcoma, there was no significant change in the relative frequency of each individual 01 within 3 months and within 3 - 12 months after enrollment across the three study periods. We concluded that despite the significant decrease in the number of AIDS-related OIs, the relative frequencies of common OIs did not change significantly after the introduction of HAART.