Aim: The aim of this study was to compare the penetration of a conventional sealant and a glass ionomer sealant with and without enameloplasty. Methods: 20 caries free extracted molar teeth were used. The teeth were divided in two groups according to the kind of material and subdivide in two groups according to the preparation of occlusal surface. The teeth were thermocycled and then each tooth was sectioned longitudinally. Fissure depth and penetration ability of the sealants was evaluated under a stereomicroscope. The ANOVA and Tukey tests were applied in order to analyze then data. Results: The penetration ability was affected only by the applied material. The mechanical preparation