Increased detection of small renal masses (SRMs) has encouraged research for non-invasive diagnostic tools capable of adequately differentiating malignant vs. benign SRMs and the type of the tumour. Multi-detector computed tomography (MDCT) has been suggested as an alternative to intervention, therefore, it is important to determine both the capabilities and limitations of MDCT for SRM evaluation. In our study, two abdominal radiologists retrospectively blindly assessed MDCT scan images of 98 patients with incidentally detected lipid-poor SRMs that did not present as definitely aggressive lesions on CT. Radiological conclusions were compared to histopathological findings of materials obtained during surgery that were assumed as the gold standard. The probability (odds ratio (OR)) in regression analyses, sensitivity (SE), and specificity (SP) of predetermined SRM characteristics were calculated. Correct differentiation between malignant vs. benign SRMs was detected in 70.4% of cases, with more accurate identification of malignant (73%) in comparison to benign (65.7%) lesions. The radiological conclusions of SRM type matched histopathological findings in 56.1%. Central scarring (OR 10.6, p = 0.001), diameter of lesion (OR 2.4, p = 0.003), and homogeneous accumulation of contrast medium (OR 3.4, p = 0.03) significantly influenced the accuracy of malignant diagnosis. SE and SP of these parameters varied from 20.6% to 91.3% and 22.9% to 74.3%, respectively. In conclusion, MDCT is able to correctly differentiate malignant versus uncharacteristic benign SRMs in more than 2/3 of cases. However, frequency of the correct histopathological SRM type MDCT identification remains low.