Statement of Problem: Application of fluoride and fissure sealant has an important cariostatic effect. The impact of topical fluoride, especially APF (Acidulated Phospheted Fluoride) gel on the restorative materials has been studied.Purpose: To assess the effect of repeated application of APF (1.23%) on the surface roughness of two sealant materials.Methods and Material: In this experimental study, 135 specimens of two sealant materials were prepared, using Aluminum cylindrical molds in three groups of 45 including: unfilled resin sealant (Clinpro), glass ionomer sealant (Triages) and glass ionomer sealant with covering of GC varnish. Then, these three groups were divided into three sub groups of 15 as follows:Group 1, 4, 7 (control): No treatment.Group 2, 8, 5:  Single application using APFGroup 3, 6, 9: Four times application using APFThe APF was applied on the experimental specimen every time for 4 minutes. Then, the samples were stored in the distilled water. Finally, the surface roughness of the sealants was measured using Profilometer. The statistical analysis was  performed by Kruskal-Wallis and Dunn tests.Results: Resin sealant exhibited no surface roughness changes following fluoride gel application (single or four applications). APF produced a statistically significant increase in the surface roughness of glass ionomer with and without varnish on them. Repeated application of APF on the surface glass ionomer specimen significantly increased their surface roughness.Conclusion: The result of the present study revealed that APF gel application significantly increases the surface roughness of glass ionomer sealants, without any effect on the resin sealant.Key words: Topical fluorides, Acidulated phosphated fluoride, Pit and fissure sealants