Objectives During the early 1990s, the economic and political situation in eastern Germany changed overnight. Here, we use the rare chance of an experiment‐like setting in humans and aim to test whether the rapid change of environmental conditions in eastern Germany in the 1990s led to a change in the sex‐specific fat distribution pattern, an endocrine‐influenced phenotypic marker. METHODS Based on a cross‐sectional data set of 6‐ to 18‐year‐old girls and boys measured between 1982–1991 and 1997–2012, we calculated a skinfold ratio of triceps to subscapular and percentage of body fat. Using linear regressions, we tested for differences in percentage of body fat and skinfold ratio between these two time periods. RESULTS We found that the percentage of body fat increased in boys and girls, and they accumulated relatively more fat on extremities than on the trunk in all BMI groups measured after 1997 as compared to those measured between 1982 and 1991. CONCLUSIONS Concurrent with drastic and rapid changes of environmental conditions, the body fat distribution of children and adolescents changed to a more feminized pattern during the early 1990s in an East German population. The changes in this endocrinologically mediated pattern might be associated with the increased exposure of individuals to endocrine‐disrupting chemicals which are known to influence the endocrine, reproductive, and immune systems in animals and humans.