The aim of this study was to detect apical inflammatory root resorption (AIRR) associated with periapical lesion using cone beam computed tomography (CBCT) and scanning electronic microscopy (SEM). This clinical study evaluated AIRR in 88 root apexes, from 52 permanent teeth of 14 patients, extracted for different reasons. The patients were submitted to a clinical interview, review of dental/medical histories and clinical/imaging examinations for treatment planning. All selected teeth showed unrestorable condition because of the extensive coronal breakdown due to carious lesions, and root canal infection associated with periapical lesions. CBCT images were obtained from the patients with the aim of diagnosing the periapical diseases which showed complex or doubtful conditions. Two examiners assessed the presence or absence of AIRR. Apices were also analyzed under SEM. Chi-square test was used to compare the imaging methods for detection of AIRR. The level of statistical significance was set at 5%. AIRR associated with root canal infection and apical periodontitis was found in 61.4% of the cases studied by using SEM, and at least half of the cases by CBCT. The microscopic analysis remains as a reference standard against the imaging method to identify AIRR.