The purpose of this study was to evaluate the clinical characteristics of patients who had both myasthenia gravis (MG) and alopecia areata (AA). Clinical information was retrospectively collected for 159 Japanese patients with MG. Human leukocyte antigen (HLA)-DQB1 and DRB1 alleles were determined by genotyping. Of 159 MG patients, six (3.7%) developed AA after the onset of MG and thymectomy. The prevalence of AA in MG patients was higher than that reported in Caucasians. The frequencies of bulbar involvement, myasthenic crisis, and thymoma were significantly higher in MG patients with AA than in those without (P = 0.007, 0.004, and 0.006, respectively). All but one patient with AA had advanced stage thymoma. Three patients with a severe form of AA (alopecia totalis) had additional autoimmune diseases: myocarditis, myositis, and pure red cell aplasia. DRB1*0901 and DQB1*0303 tended to be more frequently detected in the six MG patients with AA than in the 82 patients without it. In conclusion, a subset of MG patients who have severe neuromuscular symptoms and thymoma develop AA several years after thymectomy.