Objectives:To describe the patterns of malaria diagnosis and antimalarial use: monotherapy, missed Day 1 dosing and risk-factors. Methods: Prospective cohort of consented adult inpatients on the medical and gynaecological wards of Uganda’s 1790-bed Mulago National Referral Hospital.Results: One in five (19%, 146/762; 95% confidence interval (CI): 16% to 22%) inpatients had an admitting or discharge malaria diagnosis or both. Microscopy was requested in 77% (108/141; 95% CI: 69% to 83%) of inpatients with an admitting malaria diagnosis; results were available for 46% (50/108; 95% CI: 37% to 56%), of whom 42% (21/50; 95% CI: 28% to 57%) were positive. Artesunate (AS) only (47%, 47/100; 95% CI: 37% to 57%) was the most frequently hospital-administered antimalarial followed by quinine (Q) only (23%, 95% CI: 15% to 32%). A quarter (25%, 25/100; 95% CI: 17% to 35%) of the inpatients missed their Day 1 dose of hospital-initiated antimalarials. Nearly half (47%, 95% CI: 34% to 61%) of 57 inpatients on AS and 18%(95% CI: 4% to 32%) of 28inpatients on Q missed at least one day of dosing in Days 1-3. Number of admitting diagnoses was a significant risk-factor for missed Day 1 dosing of hospital-initiated antimalarials (OR = 2.7, 95% CI: 1.53-4.54; P-value < 0.001).Conclusions: Half the malaria microscopy results were not available; yet, the rate of testing was high. Improvement in laboratory services, procurement, prescription, dispensing and administration of antimalarials could curb missed treatment for confirmed malaria cases, monotherapy and delayed doses.