Objective: The aim of this study was to compare the effectiveness and caries-preventive effects of a fluoride varnish (Fluor Protector; 0.1% fluoride) and a chlorhexidine varnish (Cervitec; 1% chlorhexidine and 1% thymol) on initial caries of occlusal fissures and to monitor the durability of the varnishes by the use of a fluorescence system, DIAGNOdent (Dd). Method and materials: Nineteen subjects underwent professional tooth cleaning at the beginning of the study. Afterward, fluorescence measurements (baseline) were obtained from 56 test sites and 28 control sites on the central fossae of molars. Each subject had Fluor Protector and Cervitec application on randomly assigned experimental teeth, and applications were followed by Dd measurements. Measurements were repeated after 1 and 6 months. Results: There was an increase in fluorescence values immediately after application of varnish in the two test groups. One month after varnish application, Dd scores for group Fluor Protector were not significantly different from Dd scores obtained immediately after application (P = .108), whereas Dd scores for group Cervitec decreased significantly (P = .007). For both test groups, there was a significant decrease between the values obtained immediately after application and those acquired after 6 months. There was also a significant decrease between 1 month and 6 months for test groups and a slight but significant increase for the control group (P = .011). No significant difference was found between the Fluor Protector and Cervitec groups after 6 months. Conclusion: It was concluded that the Dd system may be used to monitor the existence of these two varnishes. Keywords: chlorhexidine, dental caries, diagnosis, fluoride, laser fluorescence