Obesity is a major public health problem in developed countries. We present a European project, called Identification and Prevention of Dietary and Lifestyle-induced Health Effects in Children and Infants (IDEFICS), that focuses on diet- and lifestyle-related diseases in children. This paper outlines methodological aspects and means of quality control in IDEFICS. IDEFICS will use a multicentre survey design of a population-based cohort of about 17,000 2- to 10-year-old children in nine European countries (Belgium, Cyprus, Estonia, Germany, Greece, Hungary, Italy, Spain and Sweden). The project will investigate the impact of dietary factors such as food intake and food preferences, lifestyle factors such as physical activity, psychosocial factors and genetic factors on the development of obesity and other selected diet- and lifestyle-related disorders. An intervention study will be set up in pre-school and primary school settings in eight of the survey centres. Standardised survey instruments will be designed during the first phase of the project and applied in the surveys by all centres. Standard operation procedures (SOPs) will be developed, as well as a plan for training the personnel involved in the surveys. These activities will be accompanied by a quality control strategy that will encompass the evaluation of process and result quality throughout the project. IDEFICS will develop comparable Europe-wide health indicators and instruments for data collection among young children. Establishment of a new European cohort within IDEFICS will provide a unique opportunity to document the development of the obesity epidemic in the current generation of young Europeans and investigate the impact of primary prevention in European children populations.