Objective: To investigate correlates of changes in waist-to-height ratio (WHtR) in primary school children in order to identify modifiable factors usable for prevention. Methods: Outcome evaluation of a statewide health promotion program in Baden-Württemberg, Germany. Baseline (2010) and follow-up (2011) measurements provided data for the calculation of changes in WHtR. Further information on the health and living conditions of the children were assessed in parental questionnaires. Anthropometric measures were taken in 1733 (50.8% male) first and second grade children (age at baseline 7.1 ± 0.6. years) by staff trained according to ISAK-standards. Stepwise linear regression analysis was applied to identify variables with influence on changes in WHtR. Results: According to the resulting regression model, changes in WHtR towards an increase were influenced by at least one parent being overweight/obese, at least one parent who smoked, low household income, higher age of the child and the skipping of breakfast. There was no clustering effect in schools observed. Conclusion: A promising target for prevention of gain in WHtR in primary school children is to ensure the regularity of breakfast. Smoking cessation as well as dietary improvements would not only help children's health but also the health of their parents. The socioeconomic influence on the development of an unhealthy weight status has already been acknowledged and should be extensively targeted by all of society and policy makers.