This study aimed at prospectively compared efficacy of non-contrast-enhanced (non-CE) MRI and MDCT for management of pulmonary nodules. A total of 161 patients with 200 nodules underwent MDCT and non-CE MRI (T1WI, T2WI, and STIR) in conjunction with pathological and/or more than 2 years of follow-up examinations. To compare qualitative detection rates between both modalities, all nodules were visually assessed. To compare quantitative and qualitative diagnostic capabilities of MRI, calculation of contrast ratio and visual assessment of probability for malignancy in each nodule were performed. Then, detection rate and diagnostic capability were statistically compared. Although the overall detection rate of each MR sequence (82.5%) was significantly lower than that of MDCT (97.0%, p < 0.05), that of malignant nodules showed no significant difference (p > 0.05). The diagnostic capability of STIR was significantly higher than those of other MR sequences (p < 0.05). Non-CE MR imaging was found to be as useful as MDCT for management of pulmonary nodules.