Background Furcation defects are areas of pathological bone resorption in multirooted teeth. The aim of the study was to compare the measurements of trifurcation bone loss, measured using CBCT, versus clinical measurements in order to evaluate the efficacy of CBCT as an adjunctive diagnostic tool. Material and Methods. The included patients had both CBCT scans for maxillary molars and completed periodontal charts. Clinical examination consisted of probing and detection of vertical and horizontal furcation defects. These were measured and recorded. CBCT measurements were then evaluated using the linear measuring tool in Carestream imaging software (Carestream, Rochester, USA) and iCAT (Imaging Sciences, Hatfield, USA). These measurements of the CBCT images were then documented and compared to clinical findings. The two examiners were blinded to each other's measurements. Results The most common tooth with a detected furcation defect was tooth #2 (31.7%), followed by tooth #15 (26.8%) and #3 (21.9%). The least common tooth with a detected furcation defect was #14 (19.5%). The mean values of buccal furcation for clinical and CBCT measurements were 3.01 mm and 2.6 mm, respectively. The measurements of mesial furcation were 2.5 mm and 2.2 mm for CBCT. The distal measurement of clinical examination was 2.7 mm and for CBCT was 2.44 mm. Conclusion CBCT can be used as an adjunct to clinical furcation measurements and adds useful diagnostic information to assess trifurcation defects. In addition, CBCT limited field of view (FOV) can provide relatively high-resolution images at a reduced dose that is comparable to two-dimensional imaging.