Objectives: To evaluate (1) the apical seal of root-end cavities using mineral trioxide aggregate (MTA) and glass-ionomer cement in teeth with and without cracks after ultrasonic root-end preparation and (2) the obturation efficiency of the materials in the root-end cavities. Method and Materials: Sixty teeth with root-end cavities were divided into 3 groups: teeth without cracks (-) (group A) and teeth with cracks (+) (group B). The third group (4 teeth) served as a control. Groups A and B were each divided into 2 subgroups: Groups 1A and 1B were filled with Fuji IX capsules (GC) after treatment with cavity conditioner; groups 2A and 2B were filled with white MTA (Dentsply). The teeth were immersed in india ink and cleared. Apical leakage was measured from the resection surface to the maximal point of ink infiltration. Obturation efficiency was scored as good (acceptable), irregular (acceptable), or poor (unacceptable). Statistical analysis was performed using nonparametric and Fisher exact tests. Results: Apical leakage could be arranged in the following order: Fuji IX+ > MTA+ > Fuji IX- > MTA-. Significant differences between Fuji IX- and Fuji IX+ (P .001) and between MTA- and MTA+ (P .001) were demonstrated. Fuji IX showed significantly more unacceptable fillings than did MTA (P .005). No correlation between obturation efficiency and apical leakage was demonstrated (P > .05). Conclusion: The presence of cracks originating from the root canal negatively influences the seal of root-end filling materials and is probably of major clinical importance. MTA and Fuji IX showed equal sealing capacity, but MTA showed better obturation efficiency in the root-end cavity than Fuji IX. Keywords: crack, Fuji IX, glass-ionomer cement, leakage, MTA, obturation, periradicular surgery, root-end filling, seal