BACKGROUND: The use of three-dimensional imaging has shown to provide advantages to the clinician in assessing bone morphology. The aim of this study will be to compare the diagnostic efficacy of cone beam computed tomography (CBCT) versus diagnostic clinical measurements in patients presenting with furcation involved maxillary first molars. METHODS: The study population included 20 patients with 34 maxillary first molar teeth with furcation involvement. Clinical horizontal and vertical probing measurements were compared to CBCT measurements taken by two calibrated examiners. RESULTS: Horizontal measurements showed a significant difference between Glickman class II and class III. There were no statistical significant differences with the horizontal measurements between clinical probing, bone sounding and CBCT measurements. CBCT vertical measurements were statistically greater than clinical probing measurements. CONCLUSION: The CBCT can provide similar horizontal measurements to standard clinical horizontal probing measurements and will provide a greater vertical dimension of a furcation defect to standard vertical probing measurements.