Evaluating the burden of diseases treated in hospitals in terms of (co)morbidity and financial impact is a long standing problem. Proposed solutions often rely on very sophisticated medical registration systems that are less suitable for developing countries. The authors have developed a simple prototype method for calculating financial impact and comorbidity of clinical conditions treated in a Sub-Saharan hospital environment (CALCO method) using disability weights. The developed method has been tested for 4 major clinical entities (tuberculosis, nutritional deficiencies, perinatal complications and malaria) on a dataset of 8.309 electronically registered admissions between February 1st 2009 and September 1st 2009 at the Kigali University Teaching Hospital. Results suggest that the method consists an acceptable instrument for estimating the financial burden of diseases treated in the hospital and that the proposed algorithms provide a useful formal method for quantifying hospital-bound comorbidity. The CALCO method might find its use in future implementations of Performance Based Financing (PBF) programs in Africa.