Objective: To investigate the apical sealing ability of glass ionomer and resin-based root canal obturation systems in comparison to a conventional vertical compaction of warm guttapercha. Methods: Forty-five extracted human teeth were randomly assigned into 3 groups of 15 each: a resin-based (EndoRez), a glass ionomer-based (Activ GP), and a conventional gutta-percha plus pulp sealer obturation system (GP/EWT). Apical and root canal space sealing abilities were assessed on five cross-sections 1.0 mm apart starting from the apex. Cross-section images were analysed using a focus-variation 3D scanning microscope and unsealed space was calculated as the percentage of total root canal space occupied by voids and debris. Results: EndoRez had significantly higher rate of apical leakage and deeper dye penetration as compared to GP/EWT and Activ GP. EndoRez group had also more voids and debris (22.5%) in the root canal spaces as compared to GP/EWT (10.5%) and Activ GP (10.8%). Apical leakages occurred not only along the root canal walls, but also along the gutta-percha cones with EndoRez as a result of significant polymerisation shrinkage of the resin sealer. Conclusion: Resin-based EndoRez did not form an adequate apical seal of filled root canals. Glass ionomer-based Activ GP was comparable to a vertical compaction of warm guttapercha plus EWT sealer in sealing root canal spaces. Keywords: root canal therapy, gutta-percha, glass ionomer, methacrylate resin, dye leakage