Aim To determine if Cone Beam Computed Tomography (CBCT) used in accordance with the European Commission guidelines has an impact on the diagnostic thinking confidence and therapeutic decision confidence in a population referred for endodontic problems. Methodology The study includes data collected from October 2011 until December 2012. From two different endodontic clinics consecutive patients were referred to a CBCT examination using criteria in accordance with the European Commission guidelines. The CBCT examinations were performed with similar equipment and standardized between clinics. After a thorough clinical examination and before CBCT examination, the endodontist scored the confidence for both diagnosis and therapeutic decision on a 100 mm visual analogue scale (VAS). After the CBCT examination both diagnosis and therapy plan were revised by the same dentist and a new VAS-score of confidence was performed. The VAS-scores before and after the CBCT examination were plotted for all teeth. Before and after assessments were analyzed with paired samples t-test. Results Fifty-seven patients were referred for a CBCT examination, representing 4% of all patients examined by both endodontic clinics during the study period. Four patients were excluded from the analysis as the protocol was not followed. The final data included 53 patients, and 81 teeth. For all teeth the mean score for diagnostic confidence before CBCT examination was 63 mm (SD 30). After CBCT-examination, the mean of the changes in diagnostic confidence for each patient was 23 mm (SD 27) (P < 0.01). The mean therapeutic decision confidence score Before CBCT was 67 mm (SD 25). The mean of the changes in therapeutic decision confidence after CBCT was 22 mm (SD 28) P < 0.01. Conclusions CBCT examination used in accordance with the European Commission guidelines increased the clinician’s confidence in both diagnostic thinking and therapeutic decision in a population with endodontic problems.