Background: Asymptomatic proximal coronary artery stenosis after arterial switch operation (ASO) is rare, but a potentially life-threatening condition, that is reported to appear in up to 7%. Angiography, although considered the state-of-the-art method of diagnosis, is an invasive method, but has limitations for diagnosing ostial stenosis. We report changes in Doppler flow profile and coronary flow reserve (CFR) in two asymptomatic patients (9- and 10-year old) with left main coronary artery (LMCA) ostial stenosis after ASO. Methods: Coronary flow was assessed by Transthoracic pulsed and colour-flow Doppler echocardiography (TTDE). CFR was measured in one patient using adenosine infusion (140 mcg/kg/min) over 4 minutes. CFR was calculated as the ratio of reactive hyperaemia to basal average peak velocity (APV). Both children were investigated with coronary angiography. They had myocardial Single-photon Emission Computed Tomography (SPECT), and magnetic resonance imaging (MRI) at rest and after reactive hyperaemia with adenosine infusion. Both patients had balloon dilatation and Cypher select (drug eluted) stent. Results: On echocardiogram a flame-like colour-flow diastolic signal was detected at the stenotic coronary ostia. The maximal spectral velocities during baseline conditions over the stenotic ostia were over 1.9 and 2.0 m/s (normal 30 ± 10 cm/s). The post-stenotic CFR was haemodynmically significant with value of 1.3, normal adult range 2.5–4. Coronary angiography showed a significant ostial stenosis 90% in both patients. Myocardial SPECT and MRI at rest/adenosine infusion were consistent with severe myocardial ischemia in the territory of the left coronary artery. Normal coronary angiography and coronary flow studies after stenting. Conclusion: We suggest that coronary artery flow assessment should be an integral part of the TTDE in the follow up of children with ASO. Serious coronary artery stenosis can be detected with TTDE. Assessment of CFR provides information of the physiological significance of the coronary stenosis.