Coronary microvascular dysfunction (CMD) is an independent predictor of poor prognosis in patients suffering from dilative or hypertrophic cardiomyopathy (DCM/HCM). To assess CMD, quantitative myocardial first-pass perfusion (1P) cardiovascular magnetic resonance (CMR) can be performed. Coronary sinus flow (CSF) measurements at rest and during maximal vasodilatation are an alternative and well-validated approach for the quantification of global myocardial blood flow (MBF) in CMR. Global myocardial perfusion reserve (MPR) was used to compare both methods, 1P and CSF. This measure reflects the ratio of myocardial blood flow during maximal coronary vasodilatation over rest. 1P-MPR and CSF-MPR were calculated in 17 HCM patients, 14 DCM patients and 16 controls, who underwent a stress CMR study to rule out obstructive coronary artery disease. All patients were examined on a 1.5-T system and the study protocol comprised both, first-pass myocardial perfusion imaging (MPI) and velocity-encoded (VENC) phase-contrast imaging of CSF during rest and adenosine stress. 1P-MPR was significantly decreased only in HCM patients compared to controls (1.14 vs. 1.43, p = 0.045) whereas CSF-MPR was significantly reduced in both patient groups, HCM and DCM, compared to controls (2.38 and 2.07 vs. 3.18, p = 0.041 and p = 0.032). CSF-MBF at maximal stress was significantly lower in HCM and DCM patients compared to the control group (0.11 and 1.23 vs. 1.58ml/min/g, p = 0.008 and p = 0.040). A moderate but significant correlation between CSF-MPR and 1P-MPR was observed (r = 0.39, p = 0.011). A negative correlation between LV wall thickness and CSF-MBF at rest and stress was found in the DCM group using VENC-based CSF measurements (r=- 0.64, p = 0.013 and r=- 0.69, p = 0.006)-but not using 1P-MPI. Post-proceeding analysis regarding 1P-MPR and CSF-MPR measurements required 20.1 and 6.5min, respectively (p < 0.001). The presence of microvascular disease can be non-invasively and quickly detected by VENC-based CSF-MPR measurements during routine stress perfusion CMR in both HCM and DCM patients. Compared to conventional 1P-MPI, VENC-based CSF-MPR is particularly useful in DCM patients with thinned ventricular walls.