Introduction: Due to the high prevalence of malignancy, accurate diagnosis of thyroid nodules is important. In this study, accuracy of sonography and Fine Needle Aspiration Cytology (FNAC) in diagnosis of thyroid nodules were evaluated.Methods: This cross-sectional study was performed on 80 patients with thyroid nodules referred to Qazvin hospitals in 2015. Clinical information and results of sonography, cytopathology and histopathology of the nodes were recorded. SPSS software and the Kappa Coefficient were used for analysis of data. Also the area under the curve and the confidence intervals were reported using ROCK chart.Results: Sonography results of 80 patients showed 37.5% malignancy and 52.5% benign cases. Sensitivity, specificity, PPV, NPP and accuracy of sonography were 100%, 65%, 100%, 89.6% and 91.25%, respectively. The diagnosis based on FNAC was as following: two Non-diagnostic cases, 47 benign cases, three cases of atypia with undetermined significance, seven cases of suspicious for a follicular neoplasm, six cases with suspicious malignancy and 15 malignancy cases. Sensitivity, specificity, PPV and NPP were 100%, 87%, 95% and 100%, respectively. Also the accuracy was 96.25%.Conclusion: FNAC is more accurate than sonography and it is assumed a more cost-effective method for diagnosis of thyroid nodules.