To study the association between anti-Gag and anti-Nef antibody reactivities and their correlations with disease progression, 174 HIV-1/AIDS patients were followed up for 1 year after they received triple therapy. The antibody reactivities were analyzed using a Western blot test with recombinant Gag and Nef proteins. The results showed that decreasing levels of anti-Gag or anti-Nef antibody correlate with disease progression defined by HIV-1 viral loads or T4 cell counts. After receiving triple treatment for 1 year, 8 of 38 (21.1%) Nef antibody-negative patients became positive, while only 9 of 125 (7.2%) Nef antibody-positive persons lost the antibody reactivity (p < 0.01). Therefore, HIV-1 Nef may serve as a clinical marker of disease progression.