The aim of this study was to compare the diagnostic performance of gray-scale ultrasound (US), elastography and a combination of gray-scale ultrasound and elastography (US-E) in differentiating benign and malignant thyroid nodules with respect to the level of physician experience. Three hundred fifty-eight patients with 367 thyroid nodules who underwent both gray-scale US and elastography, from November 2011 to January 2012, were included in this study. The diagnostic performance of US performed by experienced and less experienced physicians was compared. Comparisons of the diagnostic performance of US, elastography and US-E were evaluated for each group separately. Of 367 nodules, 121 were malignant and 246 were benign. When we compared the diagnostic performance of the experienced and less experienced physician groups, specificity was statistically higher in the experienced physician group for both US alone (p = 0.001) and US-E (p = 0.048). However, the experienced and less experienced physician groups did not differ significantly on other measures of diagnostic performance, regardless of modality. For the experienced physicians, the specificity and positive predictive value US were 88.0% and 76.8%, respectively; both of them were significantly higher than the corresponding values for US-E. For the less experienced physicians, specificity was significantly higher on elastography (93.8%) than on US (71.4%) (p < 0.001). However, diagnostic performance did not differ significantly between US and US-E for the less experienced physicians. Experienced physicians had superior specificity compared with less experienced physicians. The diagnostic performance of elastography and US-E was inferior compared with that of US alone, irrespective of the level of experience of the physician.