AB Background: Based on clinical trial results, the WHO recommends infant HIV testing at age 4-6 weeks and immediate antiretroviral therapy (ART) initiation in all HIV-infected infants. Little is known about the outcomes of HIV infected infants diagnosed with HIV in the first weeks of life in resource-limited settings. We assessed ART initiation and mortality in the first year of life among infants diagnosed with HIV by 12 weeks of age. Methods: Cohort of HIV-infected infants in Kinshasa and Blantyre diagnosed before 12 weeks to estimate 12-month cumulative incidences of ART initiation and mortality, accounting for competing risks. Multivariate models were used to estimate associations between infant characteristics and timing of ART initiation. Results: 121 infants were diagnosed at a median age of 7 weeks (interquartile range 6-8). The cumulative incidence of ART initiation was 46% (95% CI: 36%, 55%) at 6 months and 70% (95% CI: 60%, 78%) at 12 months. Only age at HIV diagnosis was associated with ART initiation by age 6 months, with a subdistribution hazard ratio of 0.70 (95% CI: 0.52, 0.91) for each week increase in age at DNA PCR test. The 12-month cumulative incidence of mortality was 20% (95% CI: 13%, 28%). Conclusions: Despite early diagnosis of HIV, ART initiation was slow and mortality remained high, underscoring the complexity in translating clinical trial findings and WHO guidance into real-life practice. Novel and creative health system interventions will be required to ensure that all HIV infected infants achieve optimal treatment outcomes under routine care settings.