Two different phases in disease activity are observed during the clinical course of thyroid-associated ophthalmopathy (TAO). The assessment of disease activity is important for predicting the outcome of medical management because medical treatment can be effective in the active stage. The aim of this study was to investigate whether magnetic resonance imaging (MRI) could assess the disease activity in TAO. To investigate the relation between MRI-T2 signal intensity (SI) and extraocular muscle (EOM) size, 11 patients with TAO were evaluated. EOM sizes (enlargement, volume) were measured by MRI-T1 image. T2-SI of EOM was expressed as a percentage of temporal muscle. The reduction in T2-SI was significantly positively correlated with that of EOM enlargement after treatment. Additionally, T2-SI in pretreatment showed a significant correlation with reduction in EOM volume for therapeutic effect, which indicates T2-SI in pretreatment can be one of the reliable parameters for predicting the therapeutic outcome of treatment. To investigate whether MRI-T2 pattern could predict the reversibility of diplopia, 28 patients with Graves' disease with or without ophthalmopathy were evaluated. Patients with TAO with reversible diplopia showed an uniform T2 pattern in enlarged EOM. However, in patients with irreversible diplopia caused by the mechanical limitation of EOM, MRI-T2 image showed no uniformity with a partial appearance of low T2-SI. The partial low T2-SI may indicate the progress of inactive (fibrotic) change in EOM after active (inflammatory) change. In conclusion, MRI is a useful tool for detection not only of EOM enlargement, but also disease activity in TAO. MRI-T2 SI and pattern can predict the outcome of medical management in TAO.