Failure of the apicectomies is generally attributed to dentine surface permeability and to the lack of an adequate marginal sealing of the retrofilling material which allow the percolation of microorganisms and their products from the root canal system to the periodontal region compromising the periapical healing. The purpose of this study was to evaluate the dentine and the marginal permeability after apicectomy and surface treatment with 9.6??m CO2 laser and 2.94??m Er:YAG laser irradiation. Sixty-five single rooted human endodontically treated teeth were divided in five experimental groups: group I (control), the apicectomy performed with high speed bur; group II, similar procedure to the group I followed by dentinal surface treatment with the 9.6??m CO2 laser; group III, similar procedure to group 1 followed by dentinal surface treatment with the Er:YAG laser; group IV, apicectomy and surface treatment with 9.6??m CO2 laser, and the group V, apicectomy and surface treatment with the Er:YAG laser. The analysis of methylene blue dye infiltration through the dentinal surface and the retrofilling material demonstrated that the samples from the groups which were irradiated with the lasers showed significantly less infiltration indexes than the ones from the control group. These results were compatible to the structural morphological changes evidenced through the SEM analysis. The samples from the groups II and IV (9.6??m CO2 laser) showed clean smooth surfaces, fusion and recrystallized dentine distributed homogeneously throughout the irradiated area sealing the dentinal tubules. The samples from the groups III and V (Er:YAG laser 2.94??m) also presented clean surfaces, without smear layer but slightly rough compatible to the ablationed dentine and without evidence of dentinal tubules. Through the conditions of this study, the Er:YAG 2.94??m and the 9.6??m CO2 laser used for root canal resection and dentine surface treatment showed a reduction of permeability to methylene blue dye.