Objectives: The aims of this study were to report the risk of thyroid malignancy in cases of either benign fine-needle aspiration (FNA) or without FNA performed, and to investigate possible predictive factors for thyroid malignancy in a population with recent moderately low iodine intake. Methods: All patients referred for thyroid surgery in a tertiary cancer centre between 2000 and 2016 were included (n = 3,703). After excluding cases indicating malignant histology, we included group 1: patients with benign FNA (n = 764), and group 2: patients without FNA (n = 740), leaving 1,504 eligible for further investigation. Information on age, gender, tracheal compression or dislocation, thyroid specimen weight, scintigraphy, ultrasound, medically treated thyrotoxicosis, serum stimulating thyroid hormone, indication for surgery, TNM classification, stage, and outcome were retrieved. Results: The malignancy risk was 7.6% (58/764) in group 1 and 6.8% (50/740) in group 2. Patients with T2-4 tumours constituted 2.2% (33/1,504). In the combined groups, ultrasound verified that solitary solid tumour was predictive for malignancy (p = 0.01 by χ<>2<>, and OR = 1.69, p = 0.02 in multiple logistic regression). For group 1 patients, thyrotoxicosis (which in this case was medically treated) was a significant predictive factor for malignancy (p = 0.04). Conclusions: The risk of malignancy of 7.6% and 6.8% was high, considering that patients with malignant FNA, suspicious FNA, or clinical findings indicating malignancy were excluded, and 2.2% of these malignancies were stages T2-4. In cases with solitary solid tumour on ultrasound, the risk of malignancy should not be ignored, even with benign FNA.