Autoimmune thyroid disease is a serious medical problem in which various operative procedures are performed. The objective of the study is to explore the type of applied surgical procedures in autoimmune thyroid disease, advantages and disadvantages of various procedures, and criteria they have to meet. This is retrospective clinical study on 1478 patients, operated for Graves' toxic goiter (117 males and 795 females mean age 37.7) and Hashimoto thyroiditis (27 males and 539 females mean age 50.6) from 1995 to April 2005. Cancer in Graves' disease was found in 61 patients (6.7%), papillary in 60 (occult in 53 or 6.6%) and metastatic in 1, Hashimoto thyroiditis and thyroid cancer was found in 141 patients (24.9%), papillary in 116 or 20.5% (occult in 55 or 9.7%), follicular in 2 (0.3%), Hurthle in 11 (1.9%), medullary in 8 (1.4%), anaplastic in 2 (0.3%) and lymphoma in 3 (0.5%). We performed subtotal bilateral lobectomy in 344 (312 in Graves and 32 in Hashimoto), total lobectomy on one side with subtotal on the oposite in 307 (228 in Graves and 79 in Hashimoto); out of them, in 59 patients, the remnant was left in the region of the upper pole which we called atypic lobectomy. The most common procedure, total or near by total thyroidectomy, performed in 719 (371 in Graves and 349 in Hashimoto). One side lobectomy was performed in 103 patients with Hashimoto thyroiditis. Lymph node dissection was performed in 21 (1 in Graves and 20 in Hashimoto), in all central, in 10 lateral functional and in 6 mediastinal, in 15 patients with cancer and in 6 patients with benign disease. There was no operative mortality. In Graves' disease, there was postoperative bleeding in 4 (0.4%), wound infection in 2 (0.2%) recurrent pulsy in 18 (2%) and permanent hypoparathyroidism in 13 (1.4%). In Hashimoto thyroiditis, there was postoperative bleeding in 2 (0.4%), recurrent nerve pulsy in 11 (1.9%) and permanent hypoparathyroidism in 6 (1.1%). The most common surgical procedure in autoimmune thyroid disease is total thyroidectomy which is followed by low complication rate in specialised centers. Cancer is more frequent in Hashimoto than in Graves' disease.