Indeterminate thyroid nodules (ITN) constitute the gray zone of thyroid fine-needle aspiration cytology (FNAC). About 70-80 % of ITN are later diagnosed as benign; therefore, it is very important to identify the predictors of malignancy. Aim of the study was to summarize published data about clinical risk factors for malignancy in patients with ITN and thereby provide more robust estimates of the effect of these risk factors. Sources comprised studies published through December 2012. Original articles that investigated clinical parameters as potential predictors of malignancy in ITN were identified. Two authors performed the data extraction independently. A meta-analysis of 19 relevant studies was conducted that included 3,494 patients with ITN according to FNAC. The pooled prevalence of malignancy was 28 % (95 % CI 23-33), 26 % in females and 34 % in males. The pooled OR was 1.51 (95 % CI 1.2-1.83) for males and 0.68 (95 % CI 0.53-0.88) for females. Regarding the nodule's size, the pooled OR was 2.10 (95 % CI 1.26-3.50) for nodules >4 cm in diameter. Analysis of the patient age as a risk factor was not feasible because of marked difference found between the studies. In patients with indeterminate thyroid nodules diagnosed at FNAC, the pooled rate of malignancy from 19 studies was 28 %. Patients that are male and have ITN greater than 4 cm in diameter should be considered at higher risk of cancer.