For ultrasound thyroid elastography, hand-induced freehand compression is typically applied on the neck area to induce strain in the thyroid. In contrast to this conventional approach, we have utilized natural pulsation of the carotid artery as the compression source for thyroid elastography. We have developed strain processing techniques to aid interpretation of strain induced by internal compression. Furthermore, we have developed a metric called thyroid stiffness index (TSI) to provide a more quantitative measure of thyroid tissue stiffness. From 18 patients with thyroid nodules and 5 healthy volunteers, the pulsation-induced thyroid strain was estimated and analyzed. We have found that pulsation of the carotid artery can serve as a repeatable and operator-independent compression source for thyroid elastography. TSI results from 23 subjects indicate that papillary carcinoma is stiffer than other thyroid lesions and normal thyroid glands (p<0.001), thus TSI may be useful in differentiating papillary carcinoma, the most prevalent thyroid cancer, from other lesions. With high quality strain images and a quantitative stiffness measure, thyroid elastography using natural carotid artery pulsation has good potential to provide non-invasive differential diagnosis of thyroid nodules.