In order to develop health promotion initiatives it is important to identify at what age gender and socioeconomic inequalities in health-related behaviours emerge. The aim of this longitudinal study was to analyse how health-related behaviours and weight status differed by age-group, gender, family socio-economic status and over time in three cohorts of school children. Methods. All children in grades 2, 4 and 7 in a Swedish semi-urban municipality were invited to participate (n = 1,359) of which 813 (60%) consented. At baseline and after 2 years a health questionnaire was answered by all children. Height and weight was measured. Fourteen outcomes were analysed. The main and interaction effects of time, gender and parental educational level on the health-related behaviours, weight status and body mass index standard deviation score (BMIsds) were analysed by the Weighted Least Squares method for categorical repeated measures and Analysis of Variance. Results: Nine of 12 health behaviours deteriorated over the two years: consumption of breakfast and lunch, vegetables and fruit, intake of sweetened drinks, TV viewing, club membership, being outdoors, and school recess activity; two behaviours were unchanged: intake of sweets, and active transport. Only sports participation increased with time. Girls consumed more vegetables, less sweetened drinks, performed less sports, were less physically active during recess, and had lower BMIsds, compared to boys. Those with more highly educated parents had more favourable or similar behaviours compared to those with less educated parents in 10 out of 12 health behaviours, the only exception being intake of sweets and being outdoors, and had lower BMIsds. Conclusions: This study adds to our knowledge regarding the temporal development of health behaviours and weight status in school children. Differences with regard to gender and socioeconomic status were seen already at a young age. These results contribute to our understanding of several important determinants of obesity and chronic diseases and may inform future interventions regarding how to decrease gender and social inequalities in health.