Starting in 2004, health monitoring units (GME) were established in three rural and three urban regions of the federal state Bavaria, Germany. The GME s aim is to gain current and relevant health data especially of children in Bavaria and to evaluate health promotion and prevention strategies. The first survey 2004/2005 was a cross-sectional study of the environmental health of children aged 5 to 7 years. There are data available from 3030 girls and 3319 boys (response rate 78%). This paper describes the study regions and the sociodemographic characteristics of the study population which differed substantially between urban and rural regions. The thematic focus of the survey was: (1) Social disparities in housing conditions, related environmental exposures, and children's health, (2) accidents and injuries, (3) environmental tobacco smoke exposure of children and precautionary measures of their parents, (4) nutrition, physical activity and obesity, and (5) temporal trends of the prevalence of asthma and allergies. The insights gained within the health monitoring units will contribute to the identification and quantification of health risks as well as to the establishment of intervention strategies with special focus on the needs of the public health service.