The aim of this study was to evaluate the effect of irrigation regimens on dentin microhardness at the furcation area of mandibular molars, using sodium hypochlorite and ethylenediaminetetraacetic acid (EDTA), individually and in alternation. The occlusal surface and the roots of 20 non-carious extracted human permanent mandibular molars were cut transversally and discarded. The tooth blocks were embedded in acrylic resin and randomly assigned to 4 groups (n=5) according to the irrigating regimens: 1% NaOCl solution, 17% EDTA solution, 1% NaOCl and 17% EDTA and distilled water (control). Knoop microhardness of dentin at the furcation area was evaluated. Data were analyzed using one-way ANOVA and Tukey's multiple comparison tests (α=0.05). The results of this study indicated that all irrigation solutions, except for distilled water (control), decreased dentin microhardness. EDTA did not show a significant difference with NaOCl/EDTA (p>0.05), but showed a significant difference with NaOCl (p<0.01). EDTA and NaOCl/EDTA showed a maximum decrease in microhardness. The 17% EDTA solution, either alone or in combination with 1% NaOCl reduced significantly dentin microhardness at the furcation area of mandibular molars.