To evaluate the effect of air abrasion and polishing on primary molar fissures under light microscopy. 15 exfoliated primary second molars were longitudinally sectioned and photographed under a stereomicroscope (40×; baseline evaluation). Sections were then randomly allocated into one of the two groups (n=15) and treated by either air abrasion (aluminium oxide jet) or air polishing (sodium bicarbonate jet) for 30s. After treatment, sections were washed with an air/water spray, dried with absorbent paper, and photographed as previously described (final evaluation). Baseline and final morphology were compared by two blinded examiners who evaluated changes in the width and depth of fissures. The percentage of changed fissures was analysed, and the two treatments were compared using the Mann-Whitney test (α=0.01). Both air systems resulted in fissure changes in most (93.3%) of the sections. No significant differences in fissure width changes were found between treatments, but when changes in fissure depth were evaluated, air polishing was found to be less damaging than air abrasion (p<0.01). Air abrasion and polishing cause changes to the anatomical configuration of occlusal fissures of primary molars.