AIM: (i) To evaluate the incidence of microcracks around root-end preparations completed with ultrasonic tips and their relationship with the root filling technique and thickness of surrounding dentine. (ii) To investigate the effect of rapid exposure to a water-soluble dye of Intermediate Restorative Material (IRM), Super Ethoxybenzoic Acid (sEBA) and Mineral Trioxide Aggregate (MTA), on the marginal adaptation and microleakage of root-end fillings. (iii) To describe the microstructure of the surface of root-end filling materials. METHODOLOGY: Ninety-two single-rooted teeth were divided into two groups (n = 46) according to the root canal instrumentation/filling techniques. Group 1 consisted of specimens in which canal preparation was completed using a crown-down technique and then filled with the Thermafil system (TF group); Group 2 consisted of specimens in which canal preparation was completed using a step-back technique and lateral condensation (LC group). Following root-end resection and ultrasonic cavity preparation, the samples were further divided into three subgroups (n = 24) for root-end filling with IRM, sEBA or MTA. The ultrasonic preparation time was recorded. Eight teeth were kept as positive and 12 as negative controls. Following immersion in Indian ink for 7 days, all resected root surfaces were evaluated for the presence of microcracks and the cross-sectional area of root-end surface and root-end filling were measured to evaluate the thickness of the dentinal walls. Thereafter, the samples were sectioned longitudinally so as to assess the depth of dye penetration and marginal adaptation of root-end fillings. Negative controls longitudinally sectioned were used to describe microstructural characteristics of the root-end filling materials using scanning electron microscopic (SEM) techniques. RESULTS: Although the thickness of dentinal walls between groups 1 and 2 was similar, the ultrasonic preparation time and number of microcracks were significantly higher (P < 0.001) in the TF group. Both groups had a significant correlation between microcracks and ultrasonic preparation time (P < 0.001). sEBA and IRM had better adaptation and less leakage compared with MTA. A SEM analysis displayed microstructural differences between the root-end filling materials. CONCLUSION: Microcracks can occur independently of the thickness of dentinal walls and may be associated with the prolonged ultrasonic preparation time required for the removal of the root filling during root-end cavity preparation. Although sEBA and IRM had better behaviour than MTA regarding microleakage and marginal adaptation, it is possible that exposure of MTA to a water-soluble dye before achieving full set and its porous microstructure contributed to the results.