Background Graves’ Ophthalmopathy (GO) is a complex eye and orbital disorder that is uniquely linked to Graves’ Hyperthyroidism (GH) and has traditionally been considered a cross‐reactive immune response against the thyroid stimulating hormone receptor (TSHR) in orbital tissue. However, because there is no direct evidence, such as specific TSHR antibodies or T lymphocytes targeting the orbital tissues in patients with GO compared to those without eye disease, it is important to consider alternative hypotheses for the pathogenesis of GO. The aim of this study was to identify differentially expressed genes within the thyroid of patients with GO and GH as a possible explanation for a thyroid initiated orbital autoimmunity. Methods RNA was extracted from thyroid glands of patients with GO (n = 10) and GH (n = 8) post‐total thyroidectomy. RNA samples were arrayed on Illumina® Human Ref‐8 Expression BeadChips™ representing 20 589 genes. Microarray results of selected genes were validated by quantitative PCR (qPCR) and levels of protein translation measured by Western blot analysis. Findings Two hundred and nighty‐five genes were differentially expressed between patients with GO and GH. Of these, the cardiac calsequestrin gene (CASQ2) was the most highly expressed gene in GO (2·2‐fold increase, P < 0·05). The succinate dehydrogenase flavoprotein subunit gene (SDHA) was also significantly up‐regulated in GO (P < 0·05), 1·4‐fold, while genes encoding the thyroid antigens thyroglobulin, thyroid peroxidase and TSHR were not differentially expressed. qPCR verified up‐regulation of CASQ2 and down‐regulation BMP7, CD80, IGFBP5, and MYD88 genes in GO. Western blot analysis showed that the average CASQ/GAPDH protein expression ratios for GH and GO were 1·04 and 1·03, respectively. t‐Test analysis of data generated a P‐value of 0·26, therefore no significant difference was found for CASQ protein expression in thyroid tissue between GH and GO. Interpretation The skeletal and cardiac calsequestrin proteins share 68·4% amino acid homology. Previous work has shown that RNA levels of skeletal muscle calsequestrin are 4·7 times higher in extraocular muscle (EOM) than in masticatory skeletal muscle (jaw), and cardiac calsequestrin is expressed 2·7 times more in EOM. We postulate that up‐regulation of casq2 gene in the thyroid of patients with GH may lead to the production of autoantibodies and sensitized T‐lymphocytes, which cross‐react with calsequestrin in the EOM of patients who develop ophthalmopathy.