The European IDEFICS (Identification and Prevention of Dietary- and Lifestyle-induced Health Effects in Children and Infants) Study investigates risk factors of diet- and lifestyle-related diseases in children focusing on overweight, obesity and related metabolic co-morbidities based on a standardized study protocol. In parallel, the IDEFICS study developed, implemented and evaluated strategies for the primary prevention of diet- and lifestyle-related diseases in a controlled, community-oriented design. The prospective cohort study started with a baseline survey from September 2007 to May 2008 in eight European countries, with Germany among them. During the first survey 2,065 German children aged 2-9 years passed a comprehensive examination program. Their parents answered questions on sociodemographic characteristics; media consumption; dietary, activity and sleep patterns; as well as family life and the residential environment. The results of the study will contribute to the development of harmonized European guidelines on diet and lifestyle for health promotion and disease prevention in children.