Right-atrial isomerism (RAI) is a heterotaxy syndrome with disturbances of left–right axis development resulting in complex heart malformations and anomalies of the thoracic and abdominal organs. To study the outcome of RAI, all data from patients diagnosed with this syndrome at Helsinki University Hospital between January 1976 and December of 2010 were reviewed. The outcomes were studied for 32 patients (38 % girls). The overall survival was 22 % at a median follow-up time of 13.8 years (range 0.1–33). Extracardiac malformations, mostly asplenic, occurred in 91 % of patients. Cardiac defects included dextrocardia in 44 % and common atrioventricular valve in 100 % of patients. Ventriculoarterial discordance or double-outlet ventricle was seen in 56 and 44 % of patients, respectively. Total anomalous pulmonary venous drainage occurred in 75 % and partially anomalous venous drainage in 13 % of patients. Pulmonary outflow-tract obstruction was identified in 91 % of patients. Cardiac arrhythmias were noted in nine patients (28 %), two of them with atrioventricular block. Cardiovascular surgery was performed in 71 % patients (N = 25), seven patients were inoperable. Biventricular repair was not possible in any of the patients. During long-term follow-up there was no significant difference between the patients with total, normal, or partially anomalous pulmonary venous drainage (P = 0.5). In conclusion, RAI is one of the most severe forms of congenital cardiac diseases. The prognosis remains poor despite modern surgical techniques. When RAI is identified during pregnancy, prenatal counseling, termination, or planning for prompt cardiac treatment after the birth is necessary.