Background Thymectomy is often performed on the basis of computed tomography scan findings that are suspicious for thymoma. However, the final diagnosis may be a condition such as thymic hyperplasia or lymphoma for which thymectomy is not therapeutic. The present analysis was undertaken to determine the prevalence of a “nontherapeutic” thymectomy. Methods The Nationwide Inpatient Sample from 2000 through 2009 was queried to identify patients who underwent a thymectomy. Only adult patients who underwent a total thymectomy without other associated procedures were analyzed. Patients with a diagnosis of myasthenia were excluded. A nontherapeutic thymectomy was defined as a patient who underwent thymectomy with an International Classification of Diseases, Ninth Revision diagnosis code of lymphoma, thymic hyperplasia, thymic cyst, or other benign diseases of the thymus. Results A total of 1,306 patients were identified. Overall, 72.2% (n = 943) of thymectomies were therapeutic and 27.8% (n = 363) were nontherapeutic. The most common diagnosis in the nontherapeutic group was thymic hyperplasia (n = 174). Mortality (0.32% versus 0%; p = 0.083) and overall complication rates (25% versus 17%; p < 0.001) were higher in the therapeutic group. Patients in the nontherapeutic group were younger (median age, 41 versus 56 years; p < 0.001) and more likely to undergo a video-assisted thoracoscopic surgery thymectomy (28% versus 19%; p = 0.085). Conclusions In this study, 27.8% of thymectomies were nontherapeutic, and most patients underwent an open approach. The most common benign diagnosis was thymic hyperplasia, a condition for which magnetic resonance imaging has a high predictive value. Consequently, further studies are warranted to determine the optimal evaluation of patients undergoing thymectomy for presumed thymoma.