Myasthenia gravis is an autoimmune, heterogeneous disorder, characterized by the presence of antibodies against acetylcholine receptors at the neuromuscular junction. There is a strong evidence that an individual's genetic composition is an important predisposing factor for the development of the disease. To correlate HLA class II genotypes with thymic pathology in Mexican Mestizo patients who had been subjected to thymectomy. HLA class II genes were analyzed in 60 patients and in 99 healthy ethnically matched controls. Thymic hyperplasia, atrophy, thymoma, and normal histology were encountered in 56, 33, 8 and 2% of patients, respectively. HLA-DR11 was significantly increased in patients with thymoma compared with healthy controls (pC = 0.001, OR = 13.35, 95% CI 3.5-51.3), compared with the subgroup of hyperplasia patients (pC = 0.005, OR = 15.5, 95% CI 2.78-95.58) and with the atrophy subgroup (pC = 0.04, OR = 10.5, 95% CI 1.75-70.95). This study provides the evidence of an association between HLA class II alleles with clinical and genetic heterogeneity in myasthenia gravis, particularly in those with thymoma (HLA-DR11).