Objective To prospectively evaluate 3D time-of-flight magnetic resonance angiography (3DTOF MRA) and high resolution contrast enhanced volume scan magnetic resonance angiography (CEMRA) with sensitivity encoding in diagnosing craniocervical artery stenosis. Methods Forty-six patients suspected with craniocervical artery diseases underwent MRI, 3DTOF MRA of the head and also CEMRA of the neck. The images of MRA were reconstructed with MIP and VR. The degree of arterial stenosis demonstrated on MRA was compared with that showed on digital subtraction angiography(DSA), and the data were analyzed with Spearman rank correlation coefficient (Rs). Results Excellent correlation in determining the degree of craniocervical artery stenosis existed between MRA and DSA (Rs = 0.97). With DSA as a golden standard, the sensitivity, specificity and accuracy of MRA in detecting over 50% arterial stenosis were 100%, 99.4% and 99.4% respectively. Conclusion 3DTOF MRA and CEMRA with sensitivity encoding at 3.0T are reliable and effective examinations for evaluating craniocervical artery disease. These techniques can be used as the necessary exams before DSA and can even substitute for the conventional DSA in some instances.