Background: Fine needle aspiration cytology (FNAC) cannot reliably differentiate follicular adenoma from follicular carcinoma (FC), which requires histological evidence of capsular or vascular invasion. FC is the most predominant thyroid cancer in our loco-regional environment, indicating the need for improvement in preoperative diagnostic accuracy of thyroid nodules to ensure appropriate and timely interventions. Objective: The purpose of this study was to assess the role of technetium-99m methoxyisobutylisonitrile (99mTc-MIBI) scintigraphy and ultrasonography (USG) in the differential diagnosis of thyroid nodules. Methods: Forty-two patients with hypofunctioning thyroid nodules were prospectively studied with 99mTc-MIBI scintigraphy and USG to differentiate benign from malignant nodules. An injection of 740 MBq of 99mTc-MIBI was intravenously administered, followed by semiquantitative analysis of dual-phase scans using a 4-point (0 to 3) scoring system. USG was subsequently performed and interpretation was based on some sonographic criteria for malignancy. In the following days and weeks, patients underwent FNAC followed by surgery and histopathologic examination. Results: All malignant nodules were positive on 99mTc-MIBI and all but two malignant nodules were positive on USG. The sensitivity, specificity, positive predictive value (PPV), negative predictive value (NPV) and accuracy are, respectively, 100%, 70%, 65%, 100%, and 81% for 99mTc-MIBI scintigraphy; 87%, 78%, 68%, 91% and 81% for USG; and 83%, 100%, 100%, 96% and 64% for FNAC. There was no statistically significant difference between 99mTc-MIBI scintigraphy and USG performance for both benign (p = 0.317) and malignant (p = 0.573) nodules. Conclusion: 99mTc-MIBI scintigraphy and USG are important imaging modalities in the evaluation of thyroid nodules, particularly follicular neoplasms which are frequently associated with non-diagnostic cytology.