The aim of this study is to identify the role of incomplete suppression during the first months of highly active antiretroviral treatment (HAART) to predict virologic failure in patients with high levels of HIV replication. In a retrospective, longitudinal, and multicenter study, response to HAART was assessed in treatment-naive adults with HIV RNA >100 000 copies/mL, and factors predicting failure were analyzed through regression analyses. A total of 118 patients were included. Virologic failure occurred more often in patients with >500 copies/mL at week 12 (Cox regression: Exp (B) 3.22; P = .02). HIV RNA >500 copies/mL at week 12 predicted incomplete virologic response (odds ratio [OR] = 9.33; P = .002] but not viral rebound. Major antiretroviral resistant mutations were present in 11 of 14 patients. HIV RNA >500 copies/mL at week 12 of first HAART predicts incomplete virologic response in patients with high levels of replication at baseline. Most patients carried resistance mutations at the time of failure.