Adaptation of obturation material to dentine walls is essential for the success of root canal treatment. AIM: To evaluate and compare the adaptation of gutta-percha of three obturation systems, using micro-computed tomography. METHODS: The roots of 90 central incisors were shaped with ProTaper Universal (Dentsply) files, irrigated with 1ml 5.25% sodium hypochlorite and flushed with 5ml 17% EDTA. The roots were randomly divided into: Group 1: GuttaCore obturation, Group 2: ProTaper single-cone obturation, Group 3: Thermafil obturation. All canals were sealed with AH Plus (Dentsply). A v|tome|x 240D micro-CT scanner was used to scan each root at 15μιτι resolution. The size of voids and gaps observed at 1mm, 3mm and 6mm axial sections from the apex were compared, as was the volume of cement around the gutta-percha. RESULTS: Group 2 (Protaper) had statistically significantly greater incidence of voids and of surrounding cement than either Thermafil or GuttaCore carrier based systems (Kruskal-Wallis p<0.001). CONCLUSION: Both carrier-based techniques allowed for better sealing ability in root canals compared with single-cone gutta-percha obturation although none of the materials were gap free, especially at 1mm from apex. CLINICAL SIGNIFICANCE: Both carrier-based techniques show good sealing ability and are appropriate for daily endodontic practice.