The aim of this study was to compare the responses of mineral trioxide aggregate (MTA) and combined MTA/treated dentin matrix (TDM) as direct pulp capping material. In this clinical trial study, 33 intact third molars in 11 healthy volunteers (three molars in each) were included. Partial pulpotomies were performed in a split mouth manner in two of the third molars in each patient randomly and the third tooth had used as TDM source. The coronal dentin was chopped to dentine chips and transformed to TDM using different concentrations of ethylenediamine tetraacetic acid (EDTA) solution. Pulps were directly capped by MTA alone or using a combination layering of MTA/TDM. Following 6-week clinical and radiological evaluations, each tooth was extracted and prepared for histological evaluation. There were no significant differences in the clinical and radiographic responses or in the quality of dentin bridges (P > 0.05). However, the dentin bridge was significantly thicker in MTA/TDM group than MTA group (P = 0.003). Using the combination of MTA/TDM as a pulp-dressing agent may form a thicker dentin bridge compared to MTA alone.