The purpose of this in vitro study was to compare the antimicrobial substantivity of BioPure MTAD, 2% chlorhexidine (CHX) and 2.6% sodium hypochlorite (NaOCl) in human root dentin. One hundred and ten dentin tubes prepared from human maxillary incisors were infected in vitro for 14 days with Enterococcus faecalis. The specimens were divided into five groups as follows: CHX; BioPure MTAD; NaOCl; infected dentin tubes (positive control); and sterile dentin tubes (negative control). Dentin chips were collected with round burs into Brain Heart Infusion (BHI) broth. After culturing, the number of colony-forming units (CFU) was counted. In all experimental groups, CFU was minimum after treatment (day 0), and the results obtained were significantly different from each other at any time period (P < 0.05). After treatment, the NaOCI group and BioPure MTAD group showed the lowest and highest number of CFU, respectively. In each group, the number of CFUs increased significantly by time-lapse (P < 0.05). In conclusion, the substantivity of BioPure MTAD was significantly greater than CHX and NaOCl. (J. Oral Sci. 50, 63-67, 2008)