Objectives. Assess the prevalence of thyroid nodules and predictors of malignant origin in patients with autoimmune thyroid diseases. Patients and Methods. Retrospective study including 275 patients, 198 with Graves' disease and 77 with Hashimoto's thyroiditis. Clinical and demographical data, ultrasonographical nodule characteristics, total thyroid volume and histological characteristics were recorded. Results. Graves' disease: the prevalence of thyroid nodules and thyroid carcinoma were 27.78% and 5.05%, respectively. Older age (OR = 1.054; 95% CI = 1.029-1.080) and larger thyroid volumes (OR = 1.013; 95% CI = 1.003-1.022) increased the chance of nodules. Younger age (OR = 1.073; 95% CI = 1.020-1.128) and larger thyroid volume (OR = 1.018; 95% CI = 1.005-1.030) predicted thyroid carcinoma. Hashimoto's thyroiditis: the prevalence of thyroid nodules and carcinomas were 50.7% and 7.8%, respectively. Nodules were predicted by thyroid volume (OR = 1.030; 95% CI = 1.001-1.062). We found higher number of nodules in patients with thyroid carcinoma than in those with benign nodules (3 versus 2; P = 0.03). Patients with Hashimoto's thyroiditis presented nodules more frequently than patients with Graves' disease (50.65% versus 27.28%; P < 0.001), while the prevalence of carcinoma was similar (P = 0.751). Conclusions. Larger goiter was associated with carcinoma in Graves' disease and Hashimoto's thyroiditis. Younger patients presented higher risk of papillary thyroid carcinoma in Graves' disease. The prevalence of carcinoma was similar in both conditions.