OBJECTIVES: To assess the current results and outcome of surgery in infants and children with right atrial isomerism and complex congenital heart disease. SETTING: Tertiary referral centre. METHODS: 20 consecutive children with right atrial isomerism and complex congenital heart disease underwent surgery over a 6 year period between August 1987 and July 1993. The results and outcome were analysed according to age, presentation, and surgical procedures. RESULTS: Patients were divided into two groups depending on age at presentation and initial surgery: group A comprised 11 patients who required surgical intervention in the first month of life (mean age 5 days); and group B comprised nine patients who required initial surgical intervention after the first month of life (mean age 6.8 months). Seven (64%) of the 11 patients in group A had obstructed pulmonary venous drainage and ten (91%) had pulmonary atresia. There were seven early deaths (64%), including the five patients who required systemic to pulmonary artery shunt and simultaneous repair of obstructed pulmonary veins. The long-term survival rate in this group was 18% (two of 11). Pulmonary venous obstruction was present in two (22%) of the nine patients in group B and four (44%) had pulmonary atresia. There were no early deaths. One patient died after a second palliative procedure. There was one late sudden death. Four patients had a Fontan operation with no deaths. Two of the remaining three patients meet the Fontan criteria. The long-term survival rate in this group was 78% (seven of nine). CONCLUSIONS: Surgical management of patients with right atrial isomerism who have complex congenital heart disease carries a high mortality and remains palliative. The overall survival rate was 45% (nine of 20); 18% in patients requiring surgery in the first month of life (group A) and 78% in patients requiring surgery after the first month of life (group B) (P < 0.001). Of the total of 20 patients, nine were potential candidates for a Fontan operation. Seven of these have undergone a Fontan procedure with five survivors.