Objective: The cost burden (called full cost) of providing health services at a referral, a district and a mission hospital in Ghana were determined. Methods: Standard cost-finding and cost analysis tools recommended by World Health Organization are used to analyse 2002 and 2003 hospital data. Full cost centre costs were computed by taking into account cash and non-cash expenses and allocating overhead costs to intermediate and final patient care centres. Findings: The full costs of running the mission hospital in 2002 and 2003 were US$600,295 and US$758,647 respectively; for the district hospital, the respective costs were US$496,240 and US$487,537; and for the referral hospital, the respective costs were US$1,160,535 and US$1,394,321. Of these, overhead costs ranged between 20% and 42%, while salaries made up between 45% and 60%. Based on healthcare utilization data, in 2003 the estimated cost per outpatient attendance was US$ 2.25 at the mission hospital, US$ 4.51 at the district hospital and US$8.5 at the referral hospital; inpatient day costs were US$ 6.05, US$ 9.95 and US$18.8 at the respective hospitals. User fees charged at service delivery points were generally below cost. However, some service delivery points have the potential to recover their costs. Conclusion: Salaries are the major cost component of the three hospitals. Overhead costs constitute an important part of hospital costs and must be noted in efforts to recover costs. Cost structures are different at different types of hospitals. Unit costs at service delivery points can be estimated and projected into the future.