OBJECTIVES: To determine factors that are responsible for the cost differential between private and public health facilities through the assessment of the cost per day of managing six diseases in selected health facilities in Bayelsa State, Nigeria METHODS: Prescriptions generated in three tertiary / public hospitals and three private hospitals for management of Malaria, Typhoid Fever, Essential Hypertension, Diarrhea, Pneumonia, and Rheumatoid Arthritis over a specified period were evaluated to determine direct cost of drugs. Questionnaires were used to obtain relevant data on staff wage bills, and utility bills. Data were analyzed to obtain the cost per day for each diagnosis, number of days pay required to pay for the treatment using the newly approved N18, 000.00 minimum wage by the Federal Government of Nigeria. RESULTS: Public facilities pay much higher wage bill; all facilities rely heavily on alternative power source; public facilities utilized lesser number of drugs and shorter duration; polypharmacy, co-morbidities, treatment  duration and number of drug prescribed determine cost of treatment; treatment cost for all six disease conditions was generally higher in the private facilities; Hypertension was the most costly to treat at a total cost of N20,570 for 30days requiring 36.28 days pay to afford; malaria was cheapest to treat for N227 requiring 0.4 day pay; the cost of treatment of the selected diseases are high and unaffordable CONCLUSIONS: Generally, costs of prescribed drugs were expensive in the private facilities. The costs of treatment were also generally not affordable when viewed from the point of globally accepted affordability standard. Therefore the need to make the cost of drugs cheaper for health care to be more affordable becomes imperative