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Background: Magnetic resonance (MR) black-blood thrombus imaging (BTI) is an accurate diagnostic technique for detecting deep vein thrombosis (DVT) but to date there have been no studies comparing the diagnostic performance and consistency of this technique at different field strengths. In this study, we evaluated and compared the diagnostic performance of BTI for detecting DVT at 1.5 T and 3.0 T field strengths. Methods: A total of 40 patients with DVT were enrolled in this study from November 2015 up to October 2018. All patients underwent BTI, a contrast-free T1-weighted MR imaging technique for detecting DVT, and contrast-enhanced MR venography (CE-MRV) at 1.5 T or 3.0 T field strengths. The MR data analyses used 1160 segments from the venous lumen of the 40 patients. The signal-to-noise ratio and contrast-to-noise ratio between thrombus and muscle/lumen were calculated to compare BTI at 1.5 T or 3.0 T to determine the image performance for thrombus detection at 1.5 T or 3.0 T. Two physicians blinded to the study evaluated all BTI images and calculated the overall sensitivity (SE), specificity (SP), positive predictive value (PPV) and negative predictive value (NPV), accuracy, and diagnostic consistency at 1.5 T and 3.0 T. These images and values were compared to control CE-MRV images that had been obtained by 2 senior physicians and used as reference standards. In addition, the reliability and consistency of diagnoses between observers were also evaluated. Results: Two study-blind physicians reviewed all BTI images to diagnose thrombus and to determine SE, SP, PPV, NPV, and accuracy. There were no statistical differences in SE, SP, PPV, NPV, or accuracy between the 1.5 T and 3.0 T groups. Conclusions: Black-blood thrombus imaging has high SE, SP, and accuracy for DVT diagnosis both at 1.5 T and 3.0 T field strengths. This noninvasive diagnostic technique, which does not require the use of contrast agents, can be widely used in the clinical screening of DVT and follow-up after treatment.