This study used computed tomography (CT) to compare apical canal transportation in mesiobuccal canals of maxillary molars prepared with different techniques. Sixty teeth were assigned to 3 groups (n=20), according to the technique used for root canal instrumentation: hand instrumentation with K-Flexofiles, K-Flexofiles activated by an oscillatory system and ProTaper NiTi rotary system. Pre and post-instrumentation CT images were obtained 3 mm short of the apical foramen and were superimposed to compare canal transportation. Data were analyzed statistically by ANOVA and Tukey's test using the SPSS software (α=0.05). In the buccal direction, the manual technique produced significantly less canal transportation than the oscillatory technique (p<0.05) and both were similar to the rotary technique (p>0.05). In the distal and distopalatal directions, the oscillatory technique produced more canal transportation (p<0.05). In the mesiopalatal direction, the oscillatory technique produced more canal transportation than the manual technique (p<0.05), and both were similar to the rotary technique (p>0.05). In conclusion, all techniques produced canal transportation, and the oscillatory technique produced the greatest removal of root dentin toward the innerside of the root curvature.