Background: The high incidence of renal insufficiency in patients with Peripheral Arterial Disease raises the concern for nephrogenic systemic fibrosis (NSF) with respect to contrast enhanced MRA. The risk of NSF is eliminated with non-contrast enhanced magnetic resonance angiography. The purpose of the current study is to compare image quality and diagnostic performance of non-contrast enhanced Quiescent Interval Single Shot (QISS) magnetic resonance angiography at 3T versus CT angiography for evaluation of lower extremity Peripheral Arterial Disease (PAD). Methods: 32 consecutive patients (23 male, 9 female, age range 40-81 years, average age 61.97 years) with clinically suspected lower extremity PAD underwent QISS MRA and CTA. 19 of 32 patients underwent Digital Subtraction Angiography (DSA). Image quality of MRA was compared with CTA by two radiologists with 10 and 8 years' experience according to a 4-point scale. The Kappa test was used to determine the intermodality agreement between MRA and CTA in stenosis assessment, and interobserver agreement with each method. Sensitivity and specificity of CTA and MRA in detecting hemodynamically significant stenosis (>= 50 %) were compared, with DSA serving as reference standard when available. Results: Image quality of QISS MRA was rated 3.70 +/- 0.49 by reader 1, and 3.72 +/- 0.47 by reader 2, significantly lower than that of CTA (3.80 +/- 0.44 and 3.82 +/- 0.42, P < 0.001 for both readers). Intermodality agreement between MRA and CTA was excellent for assessment of stenosis (Kappa = 0.923 +/- 0.013 for reader 1, 0.930 +/- 0.012 for reader 2). Interobserver agreement was 0.936 +/- 0.012 for CTA and 0.935 +/- 0.011 for MRA. For readers 1 and 2 respectively, the sensitivity of QISS was 94.25 and 93.26 % (versus 90.11 and 89.13 % for CTA, P > 0.05), and specificity of QISS was 96.70 and 97.75 % (versus 96.55 and 96.51 % for CTA, P > 0.05). For heavily calcified segments, sensitivity of QISS (95.83 and 95.83 %) was significantly higher than that of CTA (74.19 and 76.67 %, P < 0.05). Conclusion: QISS is a reliable alternative to CTA for evaluation of lower extremity PAD, and may be suitable as a first-line screening examination in patients with contraindications to intravenous contrast administration.