Common autoimmune disorders tend to co-exist in the same subjects and cluster in families. The objective of this study was to determine the prevalence of autoimmune co-morbidity in patients with autoimmune thyroid disease (AITD) with and without thyroid-associated orbitopathy (TAO). This was a cross-sectional study conducted at an academic tertiary referral centre. Of 1310 patients with AITD [n = 777 or 59% with Graves' disease (GD) and n = 533, 41% with Hashimoto's thyroiditis (HT)] followed at a specialized joint thyroid-eye out-patient clinic, 176 (13.4%) had an adult type of the autoimmune polyglandular syndrome, 129 (9.8%) type 1 diabetes, 111 (8.5%) coeliac disease, 60 (4.6%) type A autoimmune gastritis, 57 (4.4%) vitiligo and 25 (1.9%) Addison's disease. Coeliac disease and autoimmune gastritis were associated positively with GD [odds ratio (OR) = 2.18; P = 0.002 and OR = 6.52; P < 0.001], whereas type 1 diabetes, Addison's disease, autoimmune primary hypogonadism, alopecia areata, rheumatoid arthritis and Sjogren's syndrome were 'protective' for GD and thus linked to HT, OR = 0.49 (P < 0.001), 0.06 (P < 0.001), 0.25 (P < 0.001), 0.50 (P = 0.090) and 0.32 (P = 0.003), respectively. Of 610 (46.6%) AITD patients with TAO, 584 (95.7%) and 26 (4.3%) had GD and HT, respectively (P < 0.001). TAO was most prevalent in GD patients with coeliac disease (94%, OR = 1.87, P < 0.001). Multivariate analysis showed high OR for coeliac disease and autoimmune gastritis (3.4 and 4.03, both P < 0.001) pertaining to the association with TAO while type 1 diabetes, Addison's disease and alopecia areata were protective for TAO. In patients with TAO, coeliac disease is the most prevalent co-morbid autoimmune condition and rates are increased compared to GD patients without TAO.