Abstract The aim of this study was to compare the efficacy of grape seed extract (GSE), calcium hypochlorite [Ca(ClO)2], and sodium hypochlorite (NaOCl) irrigant solutions with rotary or reciprocating instrumentation for disinfection of root canals inoculated with Enterococcus faecalis. The mesiobuccal root canals of mandibular molars were prepared and inoculated with Enterococcus faecalis for 21 days. The roots were then randomly divided into the following eight experimental groups (n=11) according to the instrumentation technique and disinfection protocol: ProTaper Next or Reciproc R25 with sodium chloride (control group), 6% NaOCl, 6% Ca(ClO)2, or 50% GSE used for irrigation during instrumentation. The antimicrobial activity was determined on the basis of a reduction in colony-forming units (CFUs) counted on bacterial samples collected before and after root canal instrumentation and expressed as a percentage of reduction. Data were evaluated by two-way ANOVA followed by Tukey HSD post-hoc tests (p<0.05). No significant differences were observed in bacterial reduction between the ProTaper Next and Reciproc R25 systems (p>0.05), regardless of the irrigant solution used. Furthermore, all active solutions (6% NaOCl, 50% GSE, and 6% Ca(ClO)2) showed similar potential to reduce bacterial counts (p>0.05) and were significantly more effective than sodium chloride (control) (p<0.05). The results suggest that the GSE and Ca(ClO)2 have potential clinical application as irrigant solutions in endodontic therapy since they present bactericidal efficacy against Enterococcus faecalis.