The purpose of this study was to assess the in vitro the antimicrobial efficacy of chlorhexidine gluconate gel as an endodontic auxiliary chemical substance compared to sodium hypochlorite (NaOCl) and chlorhexidine gluconate solution. The antimicrobial efficacy of the tested substances was evaluated using the agar diffusion test. The growth inhibition zones produced by 0.2%, 1% and 2% chlorhexidine gel were evaluated against 5 facultative anaerobic bacteria and 4 pigmented Gram-negative anaerobes, and compared to the results obtained by NaOCl and chlorhexidine solution. The largest growth inhibition zones were produced when the test bacteria were in contact with 2% chlorhexidine gluconate gel (11.79 mm), being significantly different (p<0.05) from the growth inhibition zones produced by all NaOCl concentrations, including 5.25% (9.54 mm). However, there was no statistically significant difference (p>0.05) between the growth inhibition zones obtained with equal concentrations of chlorhexidine solution and gel. The results of this study indicate that, as far as its antimicrobial properties are concerned, chlorhexidine gel has a great potential to be used as an endodontic auxiliary chemical substance.