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Introduction Optimal management of critically ill HIV-positive patients during hospitalization and after discharge is not fully understood. This study describes patient characteristics and outcomes of critically ill HIV-positive patients hospitalized in Conakry, Guinea between August 2017 and April 2018 at discharge and 6 months post-discharge. Methods We carried out a retrospective observational cohort study using routine clinical data. Analytic statistics were used to describe characteristics and outcomes. Results 401 patients were hospitalized during the study period, 230 (57%) were female, median age was 36 (IQR: 28–45). At admission, 229 patients (57%) were on ART, median CD4 was 64 cells/mm3, 166 (41%) had a VL >1000 copies/ml, and 97 (24%) had interrupted treatment. 143 (36%) patients died during hospitalisation. Tuberculosis was the major cause of death for 102 (71%) patients. Of 194 patients that were followed after hospitalization a further 57 (29%) were lost-to-follow-up (LTFU) and 35 (18%) died, 31 (89%) of which had a TB diagnosis. Of all patients who survived a first hospitalisation, 194 (46%) were re-hospitalised at least once more. Amongst those LTFU, 34 (59%) occurred immediately after hospital discharge. Conclusion Outcomes for critically ill HIV-positive patients in our cohort were poor. We estimate that 1-in-3 patients remained alive and in care 6 months after their hospital admission. This study shows the burden of disease on a contemporary cohort of patients with advanced HIV in a low prevalence, resource limited setting and identifies multiple challenges in their care both during hospitalisation as well as during and after re-transitioning to ambulatory care.