Introduction: The aim of this study was to investigate the effects of casein phosphopeptide-amorphous calcium phosphate (CPP-ACP) application after interproximal stripping on enamel surface structures in vivo. Methods: Fifteen patients with a mean age of 15.8 years participated in this study. For each patient, the extraction of 4 first premolars was part of the orthodontic treatment plan. The patients were randomly divided into 5 groups of 3 patients. With the exception of group 1, the mesial and distal surfaces of all first premolars were stripped with a stripping disc (Komet; Gebr Brasseler, Lemgo, Germany) under air cooling and then polished with Sof-Lex polishing discs (3M Dental Products, St Paul, Minn). In group 1, no stripping was performed, and the teeth were removed immediately. In group 2, the teeth were removed immediately after the stripping. In group 3, the stripped teeth were extracted after exposure to oral conditions for 3 months. In groups 4 and 5, CPP-ACP (Recaldent Tooth Mousse; GC Europe, Leuven, Belgium) or fluoride varnish (Bifluoride 12; Voco, Cuxhaven, Germany) was applied to the stripped surfaces for 3 months, respectively, before the teeth were extracted. Surface roughness and microhardness values were evaluated with 1-way analysis of variance and Tukey HSD tests. Results: The CPP-ACP and the fluoride varnish applications increased the surface roughness and microhardness values that had been decreased by stripping. No statistically significant differences were found between groups 3, 4, and 5 for microhardness or between groups 4 and 5 for surface roughness (P > 0.5). Conclusions: The saliva and saliva plus remineralizing agents (fluoride varnish and CPP-ACP) increased the microhardness and surface roughness values of stripped enamel surfaces that had been decreased by stripping.