Background: Coronary flow velocity reserve (CFVR), defined as the ratio of maximal hyperaemic to baseline flow velocity, has been validated as a marker of physiological significance of a coronary lesion. Clinically, this parameter is measured invasively during X-ray angiography using the Doppler guide wire. With magnetic resonance (MR) imaging it is possible to quantify CFVR non-invasively. Design: The purpose of the study was to compare CFVR, acquired with MR imaging and the Doppler guide wire in patients with coronary artery disease. Methods: Twenty-two patients suffering from one- or two-vessel coronary artery disease as derived from diagnostic X-ray coronary angiography were included. Coronary flow velocity reserve was measured at baseline and during maximal hyperaemia, obtained by intravenous administration of adenosine using MR phase contrast velocity quantification. Within 2 weeks CFVR was measured invasively with a Doppler guide wire. Results: In 26 coronary arteries CFVR was acquired with both techniques. Mean CFVR in the stenosed and healthy reference arteries was 1.5 ± 0.7 and 2.7 ± 1.0 (P < 0.01) respectively for MR measurements and 1.9 ± 0.7 and 3.1 ± 0.6 (P < 0.01) respectively for Doppler measurements. Bland-Altman analysis revealed a non-significant mean difference between the two techniques of 0.4 ± 1.2. Conclusion: In a selected group of stable patients with coronary artery disease MR flow velocity quantification provides non-invasive data equivalent to the invasive Doppler guide wire data. Variability in both the MR and Doppler ultrasound measurement resulted in a significant scatter of data without systematic difference.