The aim of the study was to compare fissure sealant quality after mechanical conditioning of erbium-doped yttrium aluminium garnet (Er:YAG) laser or air abrasion prior to chemical conditioning of phosphoric acid etching or of a self-etch adhesive. Twenty-five permanent molars were initially divided into three groups: control group (n = 5), phosphoric acid etching; test group 1 (n = 10), air abrasion; and test group 2, (n = 10) Er:YAG laser. After mechanical conditioning, the test group teeth were sectioned buccolingually and the occlusal surface of one half tooth (equal to one sample) was acid etched, while a self-etch adhesive was applied on the other half. The fissure system of each sample was sealed, thermo-cycled and immersed in 5% methylene dye for 24 h. Each sample was sectioned buccolingually, and one slice was analysed microscopically. Using specialized software microleakage, unfilled margin, sealant failure and unfilled area proportions were calculated. A nonparametric ANOVA model was applied to compare the Er:YAG treatment with that of air abrasion and the self-etch adhesive with phosphoric acid (α = 0.05). Test groups were compared to the control group using Wilcoxon rank sum tests (α = 0.05). The control group displayed significantly lower microleakage but higher unfilled area proportions than the Er:YAG laser + self-etch adhesive group and displayed significantly higher unfilled margin and unfilled area proportions than the air-abrasion + self-etch adhesive group. There was no statistically significant difference in the quality of sealants applied in fissures treated with either Er:YAG laser or air abrasion prior to phosphoric acid etching, nor in the quality of sealants applied in fissures treated with either self-etch adhesive or phosphoric acid following Er:YAG or air-abrasion treatment.