The aim of this study was to find out whether differences exist in the physical development, nutritional status and psychosomatic status of children living in deprived regions of Hungary compared with the Hungarian national reference values. The Hungarian government’s decree No. 24/2003 created a complex indicator of social and economic conditions by which the country’s regions were graded into deprived and non-deprived regions. This study examined 3128 children (aged 3–18 years) living in the deprived regions and their biological status was compared with the national reference values (2nd Hungarian National Growth Study). Children’s body development was assessed via some absolute body dimensions. Nutritional status was estimated by BMI with children being divided into ‘underweight’, ‘normal’, ‘overweight’ and ‘obese’ categories. For children aged 7–18 years a standard symptoms list was used to characterize psychosomatic status. The subjects were asked to rate their health status as excellent, good, fair or poor. The body development of children living in these deprived regions was significantly retarded compared with the national references in the age groups 7–9 years and 14–17 years for boys and in the age groups 4–6 and 14–17 for girls. The prevalence of underweight was significantly higher in children and adolescents living in deprived regions (boys: 4.8%; girls: 5.9%) than the national references (boys: 2.9%; girls: 4.0%), while the prevalence of overweight and obese children did not differ between deprived regions (boys: 20.2%; girls: 19.8%) and the national references (boys: 21.5%; girls: 19.1%). Children and adolescents living in the deprived regions rated their health status worse, and experienced more psychosomatic complaints (abdominal discomfort and fear), than the national references. Although the majority of body dimensions of children in deprived regions were close to the 50th centile of the Hungarian national references, a sizeable minority (31%) were 0.20SD or more away from the median value, which has implications as to how social, medical and public welfare policy can be shaped.