A variety of autoimmune diseases has been associated with thymoma, and thymectomy does not always induce remission of these disorders. This case report describes a 50-year-old man who presented with migratory polyarthritis and an anterior mediastinal mass that proved to be a thymoma. Five months after thymectomy, the patient presented with worsening polyarthritis, hematuria, and azotemia. Based on elevated titers of antineutrophil cytoplasmic antibodies directed against myeloperoxidase and renal biopsy showing crescentic necrotizing glomerulonephritis, microscopic polyangiitis was diagnosed. After remission-induction therapy with prednisone and cyclophosphamide, articular symptoms and renal manifestations resolved. Microscopic polyangiitis was not associated previously with thymoma, and this case broadens the spectrum of autoimmune disorders seen with this tumor. Progressive disease seen after thymectomy in this patient has potential implications regarding the pathophysiological characteristics of microscopic polyangiitis and management of patients with this clinical association.