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Background: Caries is an undesirable side-effect of treatment with fixed orthodontic appliances. Therefore, it is crucial to understand how orthodontic treatment and different fluoride regimens affect caries risk and individual risk factors., Objective: To evaluate the effects of orthodontic treatment and different fluoride regimens on caries risk and caries risk factors, including cariogenic bacteria., Trial Design: Three-armed, parallel group, randomized, controlled trial., Methods: Patients referred to the Specialist Clinic of Orthodontics, Mölndal Hospital, Sweden, were distributed randomly into the following groups: group I (Control group), 1450 ppm fluoride (F) toothpaste; group II, 1450 ppm F toothpaste plus 0.2 per cent sodium fluoride (NaF) mouth rinse; and group III, 5000 ppm F toothpaste. The inclusion criteria were: age 12-20 years; and bimaxillary treatment with fixed appliances. The primary outcome variables were: caries risk; and the numbers of cariogenic bacteria. Radiographs were taken before treatment to determine the caries status. Data were collected before treatment and after 1 year with a fixed appliance. The variables were compiled into a Cariogram to assess the caries risk. Comparisons were made over time within and between the groups. The generation of randomization sequence was performed in blocks of 30. Blinding was employed during the data analysis and the caries registration., Recruitment: The clinical study duration was from October 2010 to December 2012., Results: Overall, 270 patients were randomized, of which 15 were excluded from the study. Therefore, 255 patients were included in the analyses. The caries risk increased significantly during orthodontic treatment in group I (P < 0.0001), whereas groups II and III had unchanged caries risks. All the groups showed statistically significant increases in the numbers of cariogenic bacteria., Harms: No harms were reported during the trial., Conclusions: To avoid an increased risk of caries during orthodontic treatment, everyday use of high-fluoride toothpaste (5000 ppm F) or mouth rinse (0.2% NaF) in combination with ordinary toothpaste is recommended., Registration: The trial was not registered.