Abstract This study presents an overview of the accuracy of cone beam computed tomography (CBCT) compared with micro-computed tomography (μCT) in the assessment of root canal morphology of extracted human permanent teeth. A database search in PubMed, PubMed Central, Embase, Scopus, Opengrey, Scielo and Virtual Health Library was conducted which compared root canal morphology of extracted human permanent teeth on the accuracy of CBCT with μCT. In accordance with PRISMA statement guidelines, data were extracted on study characteristics, target mediators, sampling and assay techniques and the parameters associated with obtaining the image and ability to identify the root canal morphology. Amongst 2734 records, ten fulfilled the inclusion criteria. Four studies compared the accuracy of CBCT and μCT in the assessment of root canal morphology using Vertucci's classification, with at least one CBCT group or subgroup of each study presented high agreement compared to the μCT. Six studies assessed more detailed root canal morphology, including two articles that found a lack of agreement between these imaging systems. Risk of bias was deemed low in three studies, moderate in four and high in three. CBCT can be as accurate as μCT in the assessment of several morphological features of extracted human permanent teeth; however there are some exceptions related to the more detailed morphological aspects. Voxel size likely influences the ability to detect these features, though the different aspects of exposure setting used in studies components may be confounding factors. CBCT may be considered for the assessment of root canal morphology ex-vivo.