The Survey of Sugar Intake among Children in Scotland was carried out in May to September 2006. The present study aimed to identify dietary patterns in school-aged children from the survey and investigate associations with socio-economic factors, obesity and physical activity. Habitual diet was assessed using the Scottish Collaborative Group FFQ. Height and weight were measured by trained fieldworkers. A total of 1233 FFQ were available for analysis. Dietary patterns were identified by age (5-11 and 12-17 years) and sex using principal components analysis. Associations between factor scores and socio-economic status, education level of the main food provider, physical activity levels and BMI category (based on UK 1990 charts) were examined. Three dietary patterns were identified in each age and sex group. 'Healthier' patterns loading highly for fruit and vegetables were significantly associated with higher socio-economic status and higher education levels of the main food provider whereas more 'unhealthy' patterns ('snacks' and 'puddings') were associated with lower socio-economic status and lower education levels of the main food provider. There was no consistent association between dietary patterns and BMI group or time spent in physical activity. However, inactivity (screen time) was inversely associated with 'healthier' patterns in all age and sex groups and positively associated with 'puddings' and 'snacks' in girls aged 5-11 years. Clear dietary patterns can be identified in school-age children in Scotland, which are consistently related to socio-economic factors and inactivity. This has implications for targeting health promotion at subgroups in terms of lifestyle changes required.