This paper explores the measurement of hospital costs and efficiency in a context where data is scarce, incomplete or of poor quality. It argues that there is scope for using tracers to examine and compare hospital cost structures and relative efficiency in such contexts. Two high-burden diseases, malaria and pulmonary tuberculosis, are used as tracers to calculate the average costs of inpatient care at selected tertiary hospitals. This study shows that it is feasible to prospectively collect cost data for specific diseases and explore in detail both patient cost distribution and susceptible areas for efficiency improvement. The present study found that the critical source of efficiency variation in public hospitals in Zimbabwe lies in the way hospital beds are used.