Atopic dermatitis is a common skin disorder of unknown aetiology with peak incidence in early childhood. The disease is associated with peripheral T-cell accumulation in the skin. The thymus is a key organ of the cellular immune response early in life. We hypothesized that atopic dermatitis is associated with an unbalanced establishment of the peripheral T-lymphocyte system. This cross-sectional study was performed to compare thymus sizes in patients with atopic dermatitis and healthy controls. Thirty-seven children with current atopic dermatitis were enrolled and compared with 29 healthy controls. An interview and medical examination were performed by one doctor, an ultrasound scan was performed within 3 days of the examination, and the thymus index, a marker of thymus size, was measured. The thymus index was on average 32% higher (95% CI 3%-67%) in children with active atopic dermatitis compared with healthy controls. It declined with age in both children with atopic dermatitis and healthy controls, but the reduction in size was only significant for healthy controls. We demonstrate increased size of thymus among children with active atopic dermatitis compared with healthy controls. The larger size of thymus is compatible with increased thymic activity and emission of T lymphocytes.