Background: The purpose of this study was to determine the prevalence of thyroid carcinoma in patients who underwent ultrasound-guided fine needle aspiration biopsy (USgFNA) of thyroid nodules in the island of Cyprus. Ultrasound features as well as the presence of autoimmune thyroid disease were evaluated as risk factors for malignancy. Methods: 322 consecutively examined patients (272 females/50 males, age 13-81) underwent USgFNA of thyroid nodules in a referral endocrine clinic between July 2007 and July 2009. The ultrasonographic characteristics examined were: echogenicity, margin irregularity, composition, calcifications, presence of increased vasculature and nodule size. The presence or absence of autoimmune thyroid disease was recorded. Results: From the 548 nodules examined, 74 (13.6%) were classified as THY3, 4 or 5. 75 patients (123 nodules) underwent surgical resection. 46 patients (64 nodules) proved to have thyroid carcinoma by histology. There was a significant correlation of suspicious/malignant cytology with solid composition, hypoechogenicity, irregular margins and the presence of calcifications. A significant association was also noted between the presence of positive antithyroglobulin antibodies (p < 0.05) and Graves' disease (p = 0.01) with suspicious/malignant cytology. Conclusion: The overall prevalence of thyroid cancer was 14.3%. Ultrasound characteristics were highly predictive of thyroid malignancy. Thyroid autoimmunity should be considered as a risk factor.