The purpose of this study was to compare levels of postoperative discomfort after cleaning and shaping of root canals using two protocols for removal of smear layer. Seventy-three consecutive patients requiring root canal treatment were included. At random, canals were cleaned and shaped with one of the following protocols. In group 1, 5.25% sodium hypochlorite was used as the root canal irrigant. The smear layer was removed by placing 17% EDTA in the canal(s) for 1 min followed by a 5-ml rinse with 5.25% NaOCl. In group 2, canals were irrigated with 1.3% NaOCl; the smear layer was removed by placing MTAD in the canal(s) for 5 min. Access cavities were closed with a sterile cotton pellet and Cavit. The patients recorded degree of discomfort at various time intervals after cleaning and shaping on a visual analogue scale for 1 wk. No significant statistical difference was found in the degree of discomfort between the two groups (p = 0.58).