Abstract Background Coronary anomalies (CA) include anomalous aortic origin of a coronary artery (AAOCA), anomalous coronary artery from the pulmonary artery and coronary fistulae. While outcome of natural history of anomalous left coronary artery from the pulmonary artery (ALCAPA) is poor, assessment of stress-induced ischaemia and/or arrhythmia are warranted for clinical decision making in AAOCA. Purpose The aim of this study was to establish the prevalence of ischaemia during exercise stress echocardiography (ESE) in patients with different congenital CA. Methods Patients with CA who had stress exercise echocardiography from two large tertiary cardiac centres were retrospectively recruited. Treadmill/bike exercise stress echo tests were performed and analysed according to ESC guidelines. Computed tomography (CT), magnetic resonance imaging (MRI), myocardial perfusion scintigraphy, positron emission tomography (PET) and invasive angiogram with intravascular ultrasound (IVUS) were used for CA morphology and myocardial perfusion assessment. Patients with sclerotic stenosis of >50% in any of the coronary arteries were excluded from this study. Results Total 59 patients, including 8 ALCAPA, 4 coronary fistula and 47 AAOCA (12 anomalous aortic origin of the left coronary artery (AAOLCA) and 35 anomalous aortic origin of the right coronary artery (AAORCA)) formed the study cohort. The mean age was 44±17 years. Cardiac symptoms at rest were present in 5 (63%) ALCAPA, 31 (66%) patients with with AAOCA, and none in patients with coronary fistula. Nine patients (7 ALCAPA, 1 coronary fistula and 1 AAOLCA) had undergone previous repair. Out of 47 patients with AAOCA patients, 31 (66%) had interarterial course of coronary arteries, and 8 (17%) had intramural course. A positive ESE presents in 2 (25%) ALCAPA, 1 (25%) coronary fistula patient and 1 (2%) AAOCA patient. Myocardial perfusion was assessed in 12 of 59 (20%) patients, of which 9 were AAOCA. Myocardial perfusion studies were negative in 11 patients with negative ESE tests, while only in one patient with AAOLCA myocardial perfusion defects were found on MRI and PET despite negative ESE. No major adverse cardiovascular events were observed during follow-up of patients with negative ESE. Following ESE, surgical repair of CA has been performed in 3 patients with AAORCA and in 2 patients with AAOLCA based on either symptoms attributable to anomalous coronary, evidence of myocardial ischaemia on myocardial perfusion assessment or high-risk anatomy.While 4 out of 5 repaired patients were symptomatic before repair, they became asymptomatic following repair. Conclusions Incidence of ischaemia on exercise stress echo is extremely low in AAOCA patients despite symptoms at rest and malignant anatomical features. Improving stress echo methodology by using myocardial perfusion assessment might shed a light on this discrepancy between ESE results and symptomatic status/high-risk anatomy.