Background/aim: To evaluate the malignancy risk of thyroid nodules in different clinical thyroid diseases. Materials and methods: Patients who underwent thyroidectomy between 2007 and 2014 were grouped as euthyroid, hypothyroid, and hyperthyroid. Further classification was made depending on the presence of solitary/multiple thyroid nodules. Results: Among 2870 patients, 1719 (59.9%) were euthyroid, 962 (33.5%) were hyperthyroid, and 189 (6.6%) were hypothyroid. Overall malignancy was detected in 980 (34.1%) patients. Malignancy rates were 42.1%, 42.9%, and 18.3% in the euthyroid, hypothyroid, and hyperthyroid groups, respectively (P < 0.001). A total 41.4% of patients with euthyroid nodular goiter (ENG) and 46.3% of patients with euthyroid multinodular goiter (EMNG) had thyroid malignancy (P = 0.169). Mean tumor size and capsular and vascular invasion were significantly lower in EMNG than in ENG. Among hypothyroid patients, 45.7% with solitary and 42.2% with multiple nodules were malignant (P = 0.705). When toxic nodular goiter and toxic multinodular goiter were analyzed together, malignancy rate was 24.7% (104/421), and when Graves with nodule/nodules was considered, it was 19.7% (59/299). Conclusion: In hypothyroid or euthyroid patients who underwent thyroidectomy, malignancy rate was higher than 40%, and was lower in hyperthyroid patients. Patients with multiple nodules carry a similar risk of malignancy as patients with solitary nodules, independent of the functional status.