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Abstract Background We evaluated the noncontrast MRA as an alternate method to CT angiography in assessment of patients with lower limb ischemia, 30 patients were included in a prospective cohort study; they underwent quiescent interval slice selective magnetic resonance angiography (QISS-MRA) and computed tomographic angiography (CTA). The assessment of images was evaluated by two independent consultants. The overall subjective image quality, interobserver and intermodality concordance were calculated. Results The median acquisition time in QISS-MRA was 20 min (range 18–30 min), The overall subjective image quality was rated similarly with QISS-MRA (3.13 [95% CI 2.84–3.42]) and CTA (3.23 [95% CI 2.94–3.52]; p = 0.08) with interobserver concordance for lesion ratings in QISS-MRA reached (κ = 0.987 (SD 0.006)), while for CTA it was (κ = 0.99 (SD 0.006)), while the intermodality concordance between QISS-MRA and CTA in lesion ratings were calculated on a per segment basis and was (κ = 0.944 (SD 0.013)) for reader 1 and (κ = 0.947 (SD 0.013)) for reader 2, with sensitivity 100% and specificity 97.6% Conclusions QISS-MRA is a reliable modality for assessment of patients with critical limb ischemia.