Background: At six months after initiating HAART, most HIV-infected patients have overcome initial toxic effects of the regimen and have obtained full virological suppression. We examined whether virological control during the following 12-month period predicts mortality, CD4+ cell increase, and viral suppression. Methods: Population-based follow-up study (Danish HIV Cohort Study). Patients were divided into three predictor groups according to their proportion of time with detectable (>/=400 copies/mL) HIV RNA during the period 6-18 months after HAART initiation: 0% (Group 1), 1-99% (Group 2), and 100% detectable (Group 3). Outcome: 6-year mortality and changes in CD4 count and HIV RNA. We used Kaplan-Meier survival curves, Cox´s regression and linear regression adjusted for baseline differences. Results: 2046 patients were observed for a total of 8,898 years starting at 18 months after HAART initiation. Compared with Group 1, adjusted mortality rate ratios (MRRs) were 2.6 (95% CI: 1.9-3.7) for Group 2 and 4.5 (3.2-6.4) for Group 3. 6-year survival was 92.7% (95% CI: 90.5-94.4), 85.6% (82.1-88.5), and 76.1% (70.6-80.7) in Groups 1, 2, and 3, respectively. In Group 2, treatment interruption during the first 18 months of HAART was associated with increased mortality (adjusted MRR 3.48 [95% CI: 2.10-5.79]). Mean 6-year CD4 count increase rates were 3.3 x10⁶ cells/l per month (95% CI: 2.9-3.7), 2.9 (2.5-3.3), and 2.6 (2.0-3.3) in Groups 1, 2, and 3, respectively. 96% in Group 1, 83% in Group 2, and 57% in Group 3 had HIV RNA <400 copies/mL after six years. Conclusion: Incomplete viral suppression and treatment interruptions during the first 6-18 months after HAART initiation are predictors for decreased survival, CD4+ cell progression, and viral suppression 6 years later.