ObjectivesTo evaluate and compare the obturation quality of mineral trioxide aggregate (MTA) and Biodentine placed with hand condensation or indirect ultrasonic activation technique in teeth models simulating perforating internal root resorption (IRR) using micro-computed tomographic (micro-CT) imaging.Materials and methodsStandardized models with perforating IRR cavities were created using 40 extracted single-rooted human teeth and randomly divided into four groups (n=10). The specimens were obturated with either MTA or Biodentine and the placement technique applied was either hand condensation or indirect ultrasonic activation. Micro-CT scans were performed for the volumetric analysis of voids and filling materials in the resorption cavities and apical portion of the specimens. Data were analyzed using one-way analysis of variance and paired t test.ResultsNo significant difference was observed between the groups in terms of the percentage volume of filling materials (p>0.05). The apical portion of the specimens significantly presented less percentage volume of filling materials than the resorption cavities in each group (p<0.05).ConclusionsNo placement technique produced void-free fillings in teeth with perforating IRR. There was no significant difference between the obturation quality of Biodentine and MTA. The obturation quality in the apical portion of the root canals was inferior than that in the resorption cavities.Clinical relevanceThe obturation of the apical region of teeth with perforating IRR is challenging irrespective of the material type and placement technique.