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Aim To investigate the prevalence of apical periodontitis ( AP) and root filled teeth found on cone-beam computed tomography ( CBCT) scans in a Belgian subpopulation in a retrospective cross-sectional study. Methodology At the university hospital of Leuven, 804 patients received a CBCT scan between 01/01/2013 and 01/01/2014. The investigated sample included 631 scans with a permanent dentition and a total of 11 117 teeth. Prevalences and their confidence intervals are reported and the association between treatment, position of a tooth, gender and age with AP was determined using logistic regressions. Results A total of 656 teeth (5.9%) had signs of AP and 1357 teeth (12.2%) had been root filled. AP was present in 212 of the 9760 nonroot filled teeth (2.2%) and in 444 of the 1357 root filled teeth (32.7%). Adequate root fillings were detected in approximately half (49.3%) of the root filled teeth. The prevalence of AP was 22.8% when the root filling was adequate, when scored inadequate the prevalence increased to 41%. Univariate and multivariable logistic regression analyses revealed a significant relation of tooth position and treatment with AP. No difference in the prevalence of AP between male and female patients was detected. Conclusion The prevalence of AP was comparable with findings in other epidemiological studies. Root filled teeth had significantly more AP than nonroot filled teeth. The technical quality of the root fillings had a significant impact on the presence of AP. Therefore, emphasis on the quality of work and continuing education in the field of Endodontology must be provided in Belgium. [ABSTRACT FROM AUTHOR]