Objectives: The aim of this prospective clinical study was to derive the absolute and relative costs of cone beam CT (CBCT) and panoramic imaging before removal of an impacted mandibular third molar. Furthermore, the study aimed to analyse the influence of different cost-setting scenarios on the outcome of the absolute and relative costs and the incremental costs related to surgery. Methods: A randomized clinical trial compared complications following surgical removal of a mandibular third molar, where the pre-operative diagnostic method had been panoramic imaging or CBCT. The resources implied in the two methods were measured with health economic tools. The primary outcome was total costs defined as the sum of absolute imaging costs and incremental surgery-related costs. The basic variables were capital costs, operational costs, radiological costs, radiographic costs, overheads and patient resource utilization. Differences in resources used for surgical and post-surgical management were calculated for each patient. Results: Converted to monetary units, the total costs for panoramic imaging equalized (sic)49.29 and for CBCT examination (sic)184.44. Modifying effects on this outcome such as differences in surgery time, treatment time for complications, pre- and post-surgical medication, sickness absence, specialist treatment and hospitalization were not statistically significant between the two diagnostic method groups. Conclusions: Costs for a CBCT examination were approximately four times the costs for panoramic imaging when used prior to removal of a mandibular third molar. The use of CBCT did not change the resources used for surgery, post-surgical treatment and patient complication management.