Objective: To explore the relationship between cone beam computed tomography (CBCT) measurements and direct measurements during the surgery to correct intrabony defects. Methods: Forty-four patients with 44 intrabony defects who finished initial periodontal therapy and were considered for periodontal surgery were recruited. Digital periapical radiography and CBCT was performed before the surgery. The distance from the bottom of the defect to the cementoenamel junction (CEJ-BD), the depth and mesio-distal width of the defect were measured on CBCT, periapical radiographs and during the surgery. The buccal-lingual width of the defect was only recorded on CBCT and during the surgery. Lastly, intra-surgical linear measurements were compared with measurements of radiographs and CBCT, respectively. Results: The means of the intra-surgical CEJ to BD, the depth of the defect, the mesio-distal (M-D) width and the buccal-lingual (B-L) width of the defect were 8.90 mm, 5.52 mm, 3.35 mm and 7.40 mm, respectively. Between CBCT measurements and surgical measurements the differences for the CEJ to BD (0.76 ± 1.40 mm) and the depth of the defect (0.63 ± 1.67 mm) were statistically significant, but the differences for the M-D width (-0.17 ± 0.67 mm) and the B-L width (-0.16 ± 0.65 mm) of the defect were not statistically significant. Conclusion: CBCT could provide relatively accurate measurements of the M-D width of the defect and additionally showed accurate measurements of the B-L width of the defect which periapical radiographs could not show. However, for vertical measurements of the intrabony defect (CEJ to BD and depth of the defect), when compared with measurements during the surgery, CBCT showed no advantages over periapical radiographs. A new method should be developed for accurately measuring the periodontal intrabony defects using CBCT in the future. Keywords: cone beam computed tomography, intrabony defect, linear measurement, periapical radiography