Common complications after surgery for transposition of the great arteries (TGA) include systemic ventricular dysfunction and arrhythmia after atrial baffle repair (AB) and outflow tract stenosis or regurgitation after the arterial switch (AS). Severe pulmonary hypertension (PHT) is a rarely reported problem after AB and AS. In this study we sought to evaluate the frequency of late onset severe PHT following surgical repair for TGA. We report 3 cases, 2 after AB and 1 after AS, describe the frequency of this complication and treatment response, by comparing the response to pulmonary vasodilators in this group of patients to that of idiopathic or connective tissue disease (CTD) related PHT. We currently follow 85 patients ≥17 years of age with repaired TGA; 77 after AB and 8 after AS. 3.5% of our adult congenital heart disease patients with TGA have developed late severe PHT. None of these patients demonstrated clinical improvement with Bosentan at 6 months, however 2 of 3 were stabilised with the addition of Sildenafil to initial therapy. The third patient died 4 months after the diagnosis of severe PHT, whilst waiting for heart-lung transplantation, despite Bosentan, Sildenafil and inotropic support. By contrast, of 37 patients with idiopathic or CTD related PHT commenced on Bosentan as initial therapy, 32 (86.5%) demonstrated a clinical response at 6 months; the other patients had Sildenafil as added therapy after 6 months. Our data suggest that patients with TGA and late onset PHT are less likely to achieve a clinical response on pulmonary vasodilator monotherapy (P = 0.006). Whilst more investigation is needed, our experience suggests an aggressive clinical course, often requiring combination PHT treatment.