Objectives: Plaque and stains are removed by prophylaxis methods from tooth surfaces. Since prophylaxis methods can have a detrimental effect on the surface finish of restorations, the aim of this in vitro study was to investigate the effect of three prophylaxis methods, including pumice with rubber cup, pumice with brush, and air-powder polishing device (APD) on the surface roughness of giomer. Study design: Sixty four cylindrical giomer (Beautifil II, Shofu) samples with a diameter of 6 mm and a height of 2 mm were used. Subsequent to a 3-month period of storage in distilled water at 37ºC, the samples were randomly divided into four groups of 16. In group 1 (control), no prophylaxis procedure was carried out. In groups 2 to 4 the samples were exposed to pumice with rubber cup, pumice with brush, and APD prophylaxis methods, respectively. The surface roughness of the samples was measured using a profilometer and the effect of different prophylaxis methods on surface topography was characterized by atomic force microscopy (AFM). All data were analyzed by one-way ANOVA and Duncan?s post hoc test at a significance level of P < 0.05. Results: There were statistically significant differences in surface roughness among the groups (P < 0.0005). Furthermore, in pairwise comparisons there were statistically significant differences between all the groups (P < 0.05). The roughest surfaces, in descending order, were observed with the use of APD, pumice with brush, and pumice with rubber cup. Conclusions: The use of different prophylaxis methods resulted in an increased surface roughness of giomer compared with the control group. APD prophylaxis exerted the most detrimental effects on the surface of giomer.