Autoimmune ophthalmopathy (AIO) is currently regarded as an independent genetically determined autoimmune disease characterized by lesions of the organs of vision and can be combined with other endocrine and non-endocrine autoimmune disorders. There are few publications about the combination and the differential diagnosis of myasthenia gravis and AIO. The authors present a clinical case of the combination of myasthenia gravis and autoimmune eye disease with the symptoms of the malignant exophthalmos. Our case report is of interest because the symptoms of AIO not only remain but became worse in pharmacological hypothyroidism that confirms the independence of this disease.