Background Internal voids of materials can serve a hub for microorganism and affect the sealing ability. This study aimed to evaluate the sealing performance of calcium silicate-based cements in immature teeth treated with regenerative endodontics. Methods Twenty single root canals from immature permanent premolars were prepared using regenerative endodontic protocols. The root canals were randomly divided into two groups and sealed with mineral trioxide aggregate (MTA) and Biodentine (BD). The teeth were kept in humid environment for 7 days and scanned using micro-computed tomography. The voids within the cements were segmented and visualized using image processing, incorporating the modified Otsu algorithm. The porosity of each sample was also calculated as the ratio between the number of voxels of voids and the volume of the cements. Tortuosity was also calculated using the A-star algorithm. Results Voids larger than 70 μm were predominantly observed in the top and interfacial surface of cements. The others were evenly distributed. MTA and BD showed the same level of porosity and tortuosity at interfacial surfaces. In inner surfaces, MTA showed more less porosity and tortuosity compared to BD (p < 0.05). Conclusions There were no differences in sealing performance between MTA and BD.