Purpose: To determine the role of pre-adolescents' conceptions in improving their oral health in a school-based health education programme. Materials and Methods: A school-based programme was designed as a 3-month intervention study for a representative sample of 9-year-olds (n = 338) in 12 schools in Tehran, Iran. The schools were randomly assigned to the intervention groups and controls, separately for boys' and girls' schools. Children (n = 222) underwent two kinds of oral health education programmes. The control group (n = 116) had no intervention. Positive changes in the child's oral health conceptions were evaluated after the programme as determinants of each child's oral health. Final effects of the intervention were assessed as improvements in gingival health when all index teeth with bleeding at baseline became healthy (healthy gingiva). Statistical analysis included chi-square, independent samples t-test and logistic regression models. Factor analyses were applied to the child's oral health conceptions. Results: Three factors regarding the children's oral health conceptions emerged. After the programme, boys and girls in the intervention group experienced fewer barriers to dental care than did the controls. Healthy gingiva was apparent among the boys (OR = 2.0) and the girls (OR = 4.1) in the intervention group. Girls experienced fewer barriers to dental care after the programme (OR = 1.5) and achieved more healthy gingiva, but boys' oral health conceptions showed no effect on the health of their gingiva. Conclusion: In designing health education programmes, in addition to other determinants, pre-adolescents' oral health conceptions deserve consideration. Intervention planning necessitates awareness of gender differences. Keywords: gender differences, health promotion, oral health, random allocation, school health