OBJECTIVE To compare the effectiveness of fluoride varnish and 2% chlorhexidine gel for controlling active white spot lesions (WSLs) adjacent to orthodontic brackets. METHODS Thirty-five orthodontic patients (17.2 ± 2.3 years old) presenting 60 WSLs adjacent to orthodontic brackets were enrolled in this randomized, blind, 3-armed and controlled clinical trial. The patients were randomly allocated to 1 of 3 arms: (1) two applications of 5% NaF varnish- F, with one-week interval, (2) two applications of 2% chlorhexidine gel-CHX, with one-week interval and (3) usual home care-control (CO). The WSLs were scored by using a DIAGNOdent pen. An independent examiner scored the surfaces using Nyvad criteria for caries assessment. RESULTS A total of thirty patients presenting 51 lesions completed the study. All treatments reduced the fluorescence values during the experimental period; however, F induced faster remineralization than CHX. After 3 months, 70.58 % were inactive considering all groups. DIAGNOdent pen and Nyvad presented a significant correlation. CONCLUSIONS After 3 months of treatment, F, CHX and CO were capable of controlling the WSLs adjacent to the orthodontic brackets. However, the treatment with F was capable of controlling the progression of the WSLs in a shorter period of time.