Objectives To analyse the costs of cone beam CT (CBCT) in different healthcare systems for patients with different clinical conditions. Methods Costs were calculated for CBCT performed in Cluj (Romania), Leuven (Belgium), Malmö (Sweden) and Vilnius (Lithuania) on patients with (i) a maxillary canine with eruption disturbance, (ii) an area with tooth loss prior to implant treatment or (iii) a lower wisdom tooth planned for removal. The costs were calculated using an approach based on the identification, measurement and valuation of all resources used in the delivery of the service that combined direct costs (capital equipment, accommodation, labour) with indirect costs (patients' and accompanying persons' time, "out of pocket" costs for examination fee and visits). Results The estimates for direct and indirect costs varied among the healthcare systems, being highest in Malmö and lowest in Leuven. Variation in direct costs was mainly owing to different capital costs for the CBCT equipment arising from differences in purchase prices (range €148 000-227 000). Variation in indirect costs were mainly owing to examination fees (range €0-102.02). Conclusions Cost analysis provides an important input for economic evaluations of diagnostic methods in different healthcare systems and for planning of service delivery. Additionally, it enables decision-makers to separate variations in costs between systems into those due to external influences and those due to policy decisions. A cost evaluation of a dental radiographic method cannot be generalized from one healthcare system to another, but must take into account these specific circumstances.