The effect of three methods of root-end preparation, following apical resection, on the apical seal of root-end fillings, was studied in vitro. Root canals of 116 single-rooted teeth with mature apices were prepared chemomechanically and obturated with gutta-percha and sealer. The root ends were resected with a diamond bur under water coolant and were prepared as follows: group I a size 010 round bur was used to prepare an apical cavity 2-3 mm down the long axis of the root; group II treatment as per group 1 followed by a 60-s rinse with a solution of 10:3 (10% citric acid: 3% Fe2Cl3); and group III an ultrasonic retrotip was used to prepare a 2-3 mm deep apical cavity. The root end was restored with an EBA cement. Apical leakage was determined using India ink after 7 days and 7 months. The teeth were demineralized, rendered transparent and linear dye penetration was recorded. Results showed that there was no significant difference in leakage between the groups at each time interval (P > 0.05) but there was increased leakage after 7 months (P < 0.01). Cracking of the root surface was seen most often with the ultrasonically prepared roots (P < 0.001).