Aims and Objectives: This study aims to compare the remineralizing effect of casein phosphopeptide-amorphous calcium phosphate (CPP-ACP) and fluoride varnish (FV) on the body of carious lesions in surface enamel. Materials and Methods: Two 3 mm × 3 mm areas on 37 samples of recently extracted human tooth enamel were demineralized to create artificial early carious lesions on the enamel following the methodology described by ten Cate and Duijsters. The areas were assigned randomly to two groups on which either CPP-ACP or FV were applied, after which they were subjected to a pH-cycling model to simulate intraoral conditions. Then samples were prepared for evaluation under a polarized light microscope. Data were analyzed using Student's t-test for related groups, with the SPSS statistical package. Results: No statistically significant difference was found in the depth of the body of the lesions between groups following 10 days of pH cycling. Conclusion: It was concluded that both therapeutic systems provide preventive and ultrastructural restorative treatment options which could be included in health-care policies for preventing early carious lesions.