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Purpose To evaluate root dentin pH changes using different calcium hydroxide medications in primary and permanent molar root canals. Methods Sixty primary and 60 permanent molar roots were prepared with Twisted files and assigned in two subgroups: Group1, nonsetting calcium hydroxide (n = 30); group 2, viscous vehicle-based material (ApexCal®) (n = 30). The assigned materials were delivered in root canals and then stored for 24 h, 7 days and 14 days. All specimens were transversely cut in three sections and pH change was determined by Expandable Ion Analyzer cooperating with Flat Membrane pH Electrode and Reference Half-Cell Electrode at sample root surfaces. Two-way ANOVA was used for statistical analysis. Results No significant difference was observed in primary teeth at all test periods. The mean pH values of the nonsetting calcium hydroxide group (pH10.39–10.90) were greater than those in viscous vehicle-based group (pH 9.84–10.12), but significant difference was observed only at 24 h. Among permanent teeth, the highest pH values of both materials were observed at 7 days. The pH values of the nonsetting calcium hydroxide group (pH 10.40–11.10) were greater than those in the viscous vehicle-based group (pH 9.80–10.41); however, no significant difference was observed at any test period. Conclusion The peak pH of nonsetting calcium hydroxide group was at 24 h in primary teeth and 7 days in permanent teeth. The nonsetting calcium hydroxide group showed higher pH values than those in the viscous group in both primary and permanent teeth.