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Patients with haemoglobinopathies and congenital haemolytic anaemia constitute a unique population more predisposed to developing chronic thromboembolic pulmonary hypertension (CTEPH). Although pulmonary endarterectomy (PEA) is accepted as the best treatment for CTEPH, PEA in these patients poses significant practical challenges. Apart from a few case reports, the results of PEA in this patient population have not been previously reported. The aim of this study was to review the outcome of PEA in this patient population.We performed a retrospective analysis, from our dedicated CTEPH database, of all patients who underwent PEA surgery and had abnormal haemoglobin or congenital haemolytic anaemia. We reviewed diagnosis, exchange transfusions on cardiopulmonary bypass, preoperative and postoperative pulmonary haemodynamic and functional data and outcomes for this group. Paired data analysis was performed by Student's t-test; P < 0.05 was statistically significant.Between the start of our PEA programme in 1997 and April 2015, we performed PEA in 19 patients with haemoglobinopathy or congenital haemolytic anaemia. The mean age was 52 ± 15 years. There were 9 patients with sickle cell trait, 2 with coexisting alpha+ thalassaemia trait, 2 patients with HbSC disease, 2 patients with beta-thalassaemia major, 3 patients with hereditary spherocytosis, 2 patients with stomatocytosis (one with the cryohydrocytosis subtype) and 1 patient with HbC trait. In the 9 HbAS patients, the mean HbS% was 31.9 ± 6%, and in the HbSC patients, the mean HbS% was 46.5 ± 1.3% preoperatively. To reduce this HbS to ≤20%, for safe PEA with deep hypothermic circulatory arrest, we used exchange blood transfusion. Immediately postoperatively, there was a significant improvement in pulmonary vascular resistance (938 ± 462 to 260 ± 167 dyne s cm−5; P < 0.0001). One patient died 81 days following surgery; 18 patients are alive at a median follow-up of 3.4 ± 3 years. Six months postoperatively, the patients showed significant improvement in New York Heart Association status (P < 0.0001), and in 6-min walk distance from 251 ± 111 to 399 ± 69 m (P < 0.0001).Results of PEA in this complex patient group were satisfactory. Expert haematological advice is important and exchange blood transfusions may be necessary. The presence of abnormal haemoglobin does not contra-indicate PEA surgery.