The purpose of this in vitro study was to compare the effects of a self-etch adhesive system and neodymium:yttrium-aluminum-garnet (Nd:YAG) laser application on the dentinal permeability of the furcation area of primary molars. After endodontic access, 39 extracted human deciduous molars were divided into three groups: control group (CG), no treatment; adhesive group (AG), self-etching adhesive was applied to the furcation area; laser group (LG), specimens were irradiated with Nd:YAG laser. To evaluate dentin permeability of the furcation area, we immersed the specimens in 0.5 % methylene blue dye for 4 h. Then, they were longitudinally sectioned into two halves and photographed. The images were analyzed by two qualified evaluators using TpsDig software to calculate the percentage of the dye penetration area in comparison with the total furcation area. Additional analyses by scanning electron microscopy (SEM) were performed. The analysis of variance (ANOVA), complemented by Student's t-test, showed that mean dye penetration in the LG was statistically significant lower than that in all the other groups (P < 0.05). The SEM analysis showed mostly dentinal tubules obliterated by smear layer in the CG; in the AG the smear layer was modified by the adhesive, and, in the LG, melted surfaces were observed. It can be concluded that the Nd:YAG laser was capable of reducing the dentinal permeability of the furcation area of deciduous molars.