Background Thyrotoxicosis may be caused by Graves’ disease or destructive thyroiditis. Differentiation between causes of thyrotoxicosis is crucial as management will differ. 99m Technetium (Tc)-pertechnetate thyroid scintigraphy is currently the gold standard for this purpose, however, is expensive and uses ionizing radiation. Objective To evaluate the role of color flow Doppler Ultrasound (CDU) of the superior thyroid (STA) and inferior thyroid arteries (ITA) as an inexpensive, non-invasive tool that can aid in differentiating between Graves’ disease and thyroiditis and compare it with thyroid scintigraphy. Methods Sixty-nine patients with newly-diagnosed thyrotoxicosis and 30 controls were enrolled. Thyroid functions, thyroid scintigraphy, and CDU of STA and ITA with measurements of peak systolic velocity (PSV) and end diastolic velocity (EDV), were performed. According to thyroid scintigraphy results, patients were divided into two groups: 42 patients with Graves’ disease and 27 patients with thyroiditis. Results PSV and EDV of both STA and ITA were significantly higher in patients with Graves’ disease than thyroiditis ( p -values <0.001). The STA-PSV had an equal sensitivity and specificity of 66.7%; cut-off value 76.57 cm/s, while those of STA-EDV were 73.8%, and 77.8% respectively; cut-off value 28.22 cm/s. ITA-PSV had a sensitivity and specificity of 76.2% and 77.8%, respectively; cut-off value 62.12 cm/s), while those of ITA-EDV were 78.6% and 77.8%, respectively; cut-off value 5.22 cm/s. Conclusion CDU parameters of the STA and ITA could be used as an alternative to thyroid scintigraphy for discriminating between Graves’ disease and thyroiditis.