Purpose: The aim of this multicenter study was to investigate the malignancy risk of minimally cystic thyroid nodules (MCTNs) using cyto-histopathologic diagnoses as the reference standard. Methods: From June 2015 to September 2015, 5,601 thyroid nodules (≥1 cm) from 4,989 consecutive patients who underwent thyroid ultrasonography (US) at 26 institutions were retrospectively analyzed. Each thyroid nodule was categorized according to its cystic proportion: purely solid, minimally cystic (≤10%), and partially cystic (>10%). The malignancy risk of MCTNs was compared with those of purely solid nodules and partially cystic thyroid nodules (PCTNs). The malignancy risk of MCTNs was assessed according to echogenicity and the presence of suspicious US features. Results: The prevalence of MCTNs was 22.5%. The overall malignancy risk of MCTNs was 8.8%, which was significantly lower than that of purely solid nodules (29.5%) (P<0.001), and slightly higher than that of PCTNs (6.2%) (P=0.013). The risk of malignancy associated with MCTNs was similar to that of PCTNs regardless of echogenicity or the presence of suspicious US features (all P>0.05). MCTNs were associated with a higher risk of malignancy in hypoechoic nodules than in isohyperechoic nodules and in nodules with suspicious US features than in those without suspicious US features (all P<0.001). Conclusion The malignancy risk of MCTNs was significantly lower than that of purely solid nodules. MCTNs could be categorized as PCTNs rather than as solid nodules to increase the accuracy of the risk stratification system for thyroid nodules.