Children undergoing heart transplantation in the first year of life appear in clinical observation to develop atopic eczema at an above-chance frequency despite immunosuppressive therapy with cyclosporine A. A clinical study was undertaken to clarify the extent to which those children develop atopic eczema with above-chance frequency. In this cross-sectional study, we examined 41 consecutive children after heart transplantation. Twenty-seven underwent heart transplantation in the first year of life, seven after the first birthday, and seven had cardiac surgery other than heart transplantation in the first year of life and served as a control group. Atopic eczema was diagnosed in 11 out of 27 children with heart transplant in the first year of life. No atopic eczema was diagnosed in the other two groups. Children undergoing heart transplant prior to the first birthday apparently develop atopic eczema more frequently than children whose surgery was performed after the first birthday, and also more frequently than children undergoing organ-preserving procedures, despite immunotherapy. It remains an open question whether a surgical procedure within the first months of life with subsequent immunosuppression causes an alteration in the reactivity of the immune system in these children compared to older children which promotes the occurrence of atopic eczema despite immunosuppression.