Objective: This clinical study aimed to assess the effectiveness of mineral trioxide aggregate (MTA) and calcium hydroxide (Ca[OH] 2) in the treatment of deep carious lesions using the direct complete caries excavation technique.Subjects and Methods: Hundred permanent molars/premolars were capped either with Ca (OH)2 (n = 49) or MTA (n = 51) and restored with composite resin in 73 patients. Periapical radiographs were taken prior to the treatment, at 6 months and 12 months. Two calibrated examiners clinically and radiographically assessed the periapical pathology and pulpal symptoms. Inter‑group comparisons of the observed values were analyzed using Fisher’s exact test. Significance was predetermined at α = 0.05.Results: Recall rates were 100% at 6 and 12 months. Four teeth capped with Ca(OH)2 (two each at the end of 6 and 12 months) and one tooth capped with MTA (at the end of 12 months) received endodontic emergency treatment because of symptoms of irreversible pulpitis that were clinically and/or radiographically established. There was no significant difference between the protection of the tooth vitality and pulp capping agents at 6 and 12 months (P = 0.238, P = 0.606, respectively).Conclusion: Both materials were clinically applicable at the end of 12 months.Keywords: Calcium hydroxide, complete caries excavation, deep carious lesions, mineral trioxide aggregate, pulp cappin