Background: Skipping breakfast was found to be associated with abdominal obesity in primary school children. The aim of this research was to examine factors associated with skipping breakfast in primary school children in order to develop targeted preventive measures. Methods: Baseline data assessment (2010) of a cluster-randomized controlled trial for the evaluation of a school-based health promotion program in primary school children in the state of Baden-Wurttemberg, Germany. Anthropometric measures of 1,943 primary school children aged 7.1 +/- 0.6 years (51.2% boys) were conducted according to ISAK-standards (International Standard for Anthropometric Assessment) by trained staff. Further information on the health and living conditions of the children and their parents were assessed in parental questionnaires. Generalized linear mixed regression analysis was calculated to define correlates for skipping breakfast in terms of odds ratios (OR) and 95% confidence intervals (CI). Results: According to the final regression models, significant correlates of skipping breakfast can be divided into modifiable behavioral components (high consumption of soft drinks ( OR 2.49, 95% CI 1.81; 3.43), screen media (OR 2.48, 95% CI 1.77; 3.46) and high levels of physical activity (OR 0.64, 95% CI 0.44; 0.93)) on the one hand, and more or less static socio-economic factors (migration background (OR 2.81, 95% CI 2.02; 3.91), single parenting (OR 2.13, 95% CI 1.34; 3.40), and high family education level (OR 0.42, 95% CI 0.28; 0.64)) on the other hand, and finally individual factors ( female gender (OR 1.43, 95% CI 1.03; 1.99) and having a percentage of body fat at or above the 95th percentile (OR 1.47, 95% CI 1.00; 2.17)). Conclusion: Targeted prevention should aim at health-related behaviors accompanying the habit of skipping breakfast. Focusing on vulnerable groups, characterized by not so easily modifiable socio-economic as well as individual factors, may improve results. Interventions should synergistically promote children's health and involve their parents in order to be successful. To reach all children and to avoid skipping breakfast, schools should offer regular breakfast at the start of a school day. Policy makers should support healthy eating habits at all times.