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Our study aimed at determining clinical factors associated with prolonged hospitalisation and death among children admitted with blackwater fever (BWF). We analysed 920 eligible records for the period January – December 2018 from Mbale and Soroti Regional Referral Hospitals in Eastern Uganda. The median hospitalisation was 3 (IQR: 2–5 days) days. Prolonged hospitalisation was in 251/920 (27.3%). Clinical features independently associated with prolonged hospitalisation included abdominal tenderness, body pain and mild fever. 29/920 (3.2%) died, of these 20 (69.0%) within 48 h of admission. Features of severity associated with mortality were noisy or interrupted breathing, tachypnoea, chest pain, convulsions, delayed capillary refill time (≥3 s), severe pallor, high fever (>38.5°C), altered level of consciousness, prostration and acidotic breathing.