Introduction: Botswana's AIDS response included free antiretroviral treatment (ART) since 2002, achieving 80% coverage of persons with CD4<350 cells/µl by 2009–10. We explored impact on mortality and HIV prevalence, analyzing surveillance and civil registration data.

Methods: Hospital natural cause admissions and deaths from the Health Statistics Unit (HSU) over 1990–2009, all-cause deaths from Midnight Bed Census (MNC) over 1990–2011, institutional and non-institutional deaths recorded in the Registry of Birth and Deaths (RBD) over 2003–2010, and antenatal sentinel surveillance (ANC) over 1992–2011 were compared to numbers of persons receiving ART. Mortality was adjusted for differential coverage and completeness of institutional and non-institutional deaths, and compared to WHO and UNAIDS Spectrum projections.

Results: HSU deaths per 1000 admissions declined 49% in adults 15–64 years over 2003–2009. RBD mortality declined 44% (807 to 452/100,000 population in adults 15–64 years) over 2003–2010, similarly in males and females. Generally, death rates were higher in males; declines were greater and earlier in younger adults, and in females. In contrast, death rates in adults 65+, particularly females increased over 2003–2006. MNC all-age post-neonatal mortality declined 46% and 63% in primary and secondary level hospitals, over 2003–2011. We estimated RBD captured 80% of adult deaths over 2006–2011. Comparing empirical, completeness-adjusted deaths to Spectrum estimates, declines over 2003–2009 were similar overall (47% vs. 54%); however, Spectrum projected larger and earlier declines particularly in women. Following stabilization and modest decreases over 1998–2002, HIV prevalence in pregnant women 15–24 and 25–29-years declined by >50% and >30% through 2011, while continuing to increase in older women.

Conclusions: Adult mortality in Botswana fell markedly as ART coverage increased. HIV prevalence declines may reflect ART-associated reductions in sexual transmission. Triangulation of surveillance system data offers a reasonable approach to evaluate impact of HIV/AIDS interventions, complementing cohort approaches that monitor individual-level health outcomes.