BackgroundThe World Health Organization (WHO) early warning indicators (EWIs) of HIV drug resistance (HIVDR) assess factors at individual ART sites that are known to create situations favourable to the emergence of HIVDR.MethodsIn 2014, the Namibia HIV care and treatment program abstracted the following adult and pediatric EWIs from all public ART sites (50 main sites and 143 outreach sites): On-time pill pick-up, Retention in care, Pharmacy stock-outs, Dispensing practices, and Viral load suppression. Comparisons were made between main and outreach sites and between 2014 and 2012 using the Wilcoxon signed-rank test in a matched analysis.ResultsThe national estimates were: On-time pill pick-up 81.9% (95% CI 81.1–82.8) for adults and 82.4% (81.3–83.4) for pediatrics, Retention in care 79% retained on ART after 12 months for adults and 82% for pediatrics, Pharmacy stock-outs 94% of months without a stock-out for adults and 88% for pediatrics, and Dispensing practices 0.01% (0.001–0.056) dispensed mono- or dual-therapy for adults and 0.01% (0.001–0.069) for pediatrics. Viral load suppression was significantly affected by low rates of Viral load completion. Main sites had higher On-time pill pick-up than outreach sites for adults (p<0.001) and pediatrics (p<0.001), and no difference between main and outreach sites for Retention in care for adults (p = 0.761) or pediatrics (p = 0.214). From 2012 to 2014 in adult sites, On-time pill pick-up (p = 0.001), Retention in care (p<0.001), and Pharmacy stock-outs (p = 0.002) worsened. In pediatric sites, On-time pill pick-up (p<0.001) and Pharmacy stock-outs (p = 0.012) worsened.ConclusionsResults of EWIs monitoring in Namibia provide evidence about ART programmatic functioning and contextualize results from national surveys of HIVDR. These results are worrisome as they show a decline in program performance over time. The national ART program is taking steps to minimize the emergence of HIVDR by strengthening adherence and retention of patients on ART, reducing stock-outs, and strengthening ART data quality.