Background: Our goal was to elucidate the differences in degree of technical difficulty of thyroidectomy in patients with autoimmune thyroid diseases. Methods: Charts of adult patients who had undergone thyroidectomy were reviewed.Patients with Hashimoto's Thyroiditis (HT) or Graves' Disease (GD) were individually compared to a control group of patients with early stage malignancy or goiter. Results: The HT (n = 65) group was significantly more likely to have friable (P = .001) and fibrotic (P < .001) thyroids, longer operative times (P = .02), and a 22-modifier (P = .005). The GD (n = 169) group was significantly more likely to have friable (P < .001), vascular (P < .001), fibrotic (P = .038), and heavy (P = .002) thyroids, longer operative times (P = .03), increased length of stay (P = .01) and a 22-modifier (P = .01). Conclusion: Our experience at an institution with a high-volume thyroid practice demonstrates that patients with autoimmune thyroid disease have consistent qualitative changes of the thyroid and significantly increased operative times and surgical difficulty.