Objective: To measure quality of life in children with pulmonary atresia and intact ventricular septum, and make comparisons with a healthy group of children from the general Swedish population. An additional aim was to compare quality of life in two subgroups, children undergoing biventricular and univentricular repair, the latter by establishment of the Fontan circulation. Methods: Quality of life was measured using a mailed questionnaire, taking into consideration the three spheres of personal, interpersonal, and external living conditions. In all, 52 children received the questionnaire, and the answers were compared with those of a random sample of 1856 healthy Swedish children. Results: We received responses from 42 children and parents. The overall differences between groups were small, and no difference was found when comparing the children undergoing univentricular as opposed to biventricular surgical repair. In terms of personal quality of life, we found a higher level of psychosomatic complaints, and lower satisfaction with their own and parent–child activities, in those with the congenital anomaly than in their normal peers. In terms of the interpersonal sphere, more time was available for those with malformed hearts, but the experience of support from the relatives was significantly lower. Conclusions: Overall, quality of life was equal between children with pulmonary atresia and intact ventricular septum and the children in the reference group. The personal psychological conditions were less favourable for children with pulmonary atresia and intact ventricular septum. The perceived lack of support from relatives was also higher in these families. No difference was found when comparing the children undergoing univentricular and biventricular surgical repair.