The aim of this analysis was to investigate the strength of the association between sugar intake and treatment for dental decay in children in Scotland, and the impact of tooth brushing frequency on this association. The Survey of Sugar Intake among Children in Scotland was carried out in 2006 in those aged 3-17 years. Diet was assessed using the Scottish Collaborative Group FFQ, and interviews were carried out by trained fieldworkers who asked about dental health. A total of 1700 interviews were carried out, and 1512 FFQ were returned. Of the children, 56% had received treatment for decay (fillings or teeth removed due to decay). Intake of non-milk extrinsic sugars (NMES), but not total sugar, increased the risk of having had treatment for decay: adjusted OR 1.84 (95% CI 1.28, 2.64) for the highest ( ≥ 20.0% food energy) v. lowest ( ≤ 14.8% food energy) tertile of NMES intake. This raised risk remained in children who reported brushing their teeth at least twice a day. Compared with children who reported brushing their teeth at least twice a day and were in the lowest tertile of NMES intake, children who reported brushing their teeth once a day or less and were in the highest tertile of NMES intake were over three times more likely to have received treatment for decay (adjusted OR 3.39, 95% CI 1.97, 5.82). In order to improve dental health in children in Scotland, dental health strategies must continue to stress the importance of both reduced NMES intake and good oral hygiene.