Failure of apicectomies is generally attributed to dentine surface permeability as well as to the lack of an adequate marginal sealing of the retrofilling material, which allows the percolation of microorganisms and their products from the root canal system to the periodontal region, thus compromising periapical healing. The purpose of this study was to evaluate dentine and the marginal permeability after apicectomy and surface treatment with 9.6 micro m TEA CO(2) or Er:YAG 2.94 micro m laser irradiation. Sixty-five single rooted human endodontically treated teeth were divided into five experimental groups: group I (control), apicectomy with high speed bur; group II, similar procedure to that of group I, followed by dentinal surface treatment with 9.6 micro m CO(2) laser; group III, similar procedure to group I followed by dentinal surface treatment with Er:YAG laser 2.94 micro m; group IV, apicectomy and surface treatment with CO(2) 9.6 micro m laser; and group V, apicectomy and surface treatment with Er:YAG laser 2.94 micro m. The analysis of methylene blue dye infiltration through the dentinal surface and the retrofilling material demonstrated that the samples from the groups that were irradiated with the lasers showed significantly lower infiltration indexes than the ones from the control group. These results were compatible with the structural morphological changes evidenced through SEM analysis. Samples from groups II and IV (9.6 micro m CO(2)) showed clean smooth surfaces, fusion, and recrystallized dentine distributed homogeneously throughout the irradiated area sealing the dentinal tubules. Samples from groups III and V (Er:YAG 2.94 micro m) also presented clean surfaces, without smear layer, but roughly compatible to the ablationed dentine and without evidence of dentinal tubules. Through the conditions of this study, the Er:YAG 2.94 micro m and the 9.6 micro m CO(2) laser used for root canal resection and dentine surface treatment showed a reduction of permeability to methylene blue dye.