<b><i>Introduction:</i></b> Almost half of the cystic renal lesions are still overdiagnosed and overtreated. New clinical and radiological parameters are needed to distinguish the malignant Bosniak 3 lesions from the benign ones. We aimed to evaluate the clinical and radiological parameters that may be related to malignancy risk for Bosniak category 3 renal cysts. <b><i>Materials and Methods:</i></b> Patients who underwent surgical resection of a histopathologically confirmed Bosniak 3 renal cyst between March 2007 and September 2019 were evaluated. Two experienced uro-radiologists have reevaluated the last preoperative computed tomography and/or MRI images of the patients and reclassified the lesions according to the Bosniak classification. They also reported cystic features such as nodularity, septation, focal thickening, enhancement, and calcification. Clinical, pathological, and oncological outcomes were recorded. Then patients were divided into 2 groups as Group 1 (benign pathology) and Group 2 (malignant pathology) according to final histopathological report. <b><i>Results:</i></b> A total of 79 patients were included in this study. Mean follow-up time was 47 ± 34 months. There were 30 patients in Group 1 and 49 patients in Group 2. Hypertension (<i>p</i> = 0.001) and smoking history (<i>p</i> = 0.008) were more common in malignant group. Among the radiological findings, lower tumor diameter (<i>p</i> = 0.024), presence of cyst wall enhancement (<i>p</i> = 0.025), presence of nodularity (<i>p</i> = 0.002), and presence of focal thickening (<i>p</i> = 0.031) were found to be statistically significant for malignancy. Most of the tumors were at pathological T1 stage and Fuhrmann Grade 1–2. Only nodularity was found to be independent predictive factor for malignancy in multivariate analysis. <b><i>Conclusion:</i></b> Clinical factors including hypertension and smoking, radiological factors including lower lesion size, cyst wall enhancement, nodularity, and focal thickening were predictors for malignancy of Bosniak 3 cysts.