Thyroid associated ophthalmopathy (TAO) is an autoimmune disorder often coexisting with Graves’ disease, where clinical symptoms result from the inflammatory reactions occurring in retroorbital tissue. The mechanisms responsible for disease evolution have not been precisely recognized. Infectious, environmental, immune and genetic factors are likely to take part in the development of the disease. Recently, intensive research of cytokines influence on thyroid cells and retroorbital tissue have been undertaken. The cytokines group which takes part in TAO pathogenesis is very large, but the role of each individual cytokine is not yet fully known. The gene polymorphisms of these cytokines are also being investigated. The results of the studies obtained so far are not explicit. However, it can be expected that in the near future a cytokines genes polymorphism estimation in patients with thyroid associated ophthalmopathy and Graves’ disease will be a helpful means to choose the treatment method and to establish the prognosis.