OBJECTIVE: To estimate the early and long-term mortalities and associated risk factors in adults receiving highly active antiretroviral therapy (HAART) in Thailand. DESIGN: A prospective observational cohort study. METHODS: Previously untreated adults starting HAART in 2002-2009 were followed-up in 43 public hospitals. Kaplan-Meier probability of survival was estimated up to 5 years of therapy. Factors associated with early (≤6 months) and long-term (>6 months) mortalities were assessed using Cox regression analyses. RESULTS: A total of 1578 adults received HAART (74% women; median age, 33 years; CD4 cell count, 124/mL), with a median follow-up of 50 months (interquartile range, 41-66). Eighty-nine patients (6%) died (37 occurred ≤6 months and 52 occurred >6 months) and 183 (12%) were lost to follow-up. Probability of survival [95% confidence interval (CI)] was 97.5% (96.7% to 98.2%) at 6 months, 96.6% (95.6% to 97.4%) at 1 year, and 93.5% (91.9% to 94.8%) at 5 years. Probability of being alive and on follow-up was 80.8% (78.5% to 82.8%) at 5 years. Early mortality was associated with anemia [adjusted hazard ratio (aHR) 3.6, 95% CI: 1.7 to 7.5] and low CD4 count (aHR 1.6, 95% CI: 1.1 to 2.2 per 50 cells decrease) at treatment initiation. Long-term mortality was associated with persistent anemia (aHR 4.9, 95% CI: 2.1 to 11.6), CD4 increase from baseline <50 cells per cubic millimeter (aHR 3.1, 95% CI: 1.6 to 5.7), and viral load >1000 copies per milliliter (aHR 2.8, 95% CI: 1.3 to 6.1) at 6 months of HAART; male gender; and calendar year of enrollment. CONCLUSIONS: Early mortality was associated with anemia and severe immunosuppression at initiation of therapy. Long-term mortality was associated with persistent anemia, CD4 count increase, and virological response at 6 months of therapy over baseline characteristics, highlighting the importance of laboratory monitoring.