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Objective Patients with type 2 diabetes (T2DM) generally experience a higher incidence of cancer. However, the association between T2DM and thyroid cancer is inconclusive. Methods Case-control prospective study, where 722 patients were screened for T2DM and prediabetes (PDM) and underwent thyroid ultrasound and biochemical tests. The patients were assigned to groups of PDM (n = 55), T2DM (n = 79) or a non-diabetes group (NDM) (n = 588). Fine-needle aspiration biopsy was carried out in 263 patients. Histological examinations were done for 109 patients after surgery, with findings of 52 benign (BS) and 57 malignant tumors (MS). Results Thirty-three percent of patients with T2DM and especially PDM were newly diagnosed by our screening: 6.5% with T2DM and 72% with PDM, respectively. The percentage of thyroid cancers did not significantly differ between the groups (χ2 test = 0.461; P = 0.794). Relevant positive thyroid predictors for T2DM (t-statistic = 25.87; P < 0.01) and PDM (21.69; P < 0.01) contrary to NDM (−26.9; P < 0.01) were thyroid volume (4.79; P < 0.01), thyroid nodule volume (3.25; P < 0.01) and multinodular thyroid gland (4.83; P < 0.01), while negative relevant predictors included the occurrence of autoimmune thyroid disease (AITD) (−2.01; P < 0.05). Conclusion In general, we did not observe an increased risk for thyroid cancer in the diabetic and prediabetic groups in comparison to controls, in spite of well-established increased risk for other malignancies. Structural and benign changes such as larger and multinodular thyroid glands, in comparison to autoimmune thyroid disease, are present more often in diabetics.