To assess the accuracy of cone beam computed tomography (CBCT) in detecting furcation involvement (FI) in maxillary molars. Fourteen patients with generalized advanced chronic periodontitis were consecutively recruited and treated non-surgically. In maxillary molars considered for furcation surgery due to increased FI and/or increased probing pocket depths during re-evaluation, CBCT was performed and the degree of FI was evaluated from the CBCT images. Furcation surgery was performed in 25 maxillary molars. Intra-surgical FI assessments were compared with data derived from CBCT images. Overall, 84% of the CBCT data were confirmed by the intra-surgical findings (weighted kappa=0.926, 95% confidence interval: 0.681-1.0). While 14.7% (11 sites) were underestimated (CBCT less than intra-surgical value), in only 1.3% (one site) did the CBCT data lead to an overestimation compared with the intra-surgical analysis. The agreement between both assessments was the highest in distopalatal furcation entrances, followed by buccal and mesiopalatal. CBCT images demonstrate a high accuracy in assessing the loss of periodontal tissue and classifying the degree of FI in maxillary molars.