Objective Transglutaminase antibody (TGA) is specific for celiac disease (CD). Some studies have shown that CD is associated with autoimmune thyroid diseases (AITD) and autoimmune type 1 diabetes (T1DM). T1DM, AITD and CD are components of autoimmune polyendocine syndrome(APS) type Ⅱ.We investigated the relationships among T1DM, AITD and CD. Methods We detected the titers of TGA, glutamic acid decarboxylase antibody (GADA), insulinoma associated protein-2 antibody (IA-2A), zinc transporter 8 antibody (ZnT8A) and TSH receptor antibody (TRAb) in patients with T1DM and AITD. Results TGA level in T1DM group and AITD group is significantly higher than that in type 2 diabetes (P < 0.01) and non-autoimmune thyroid diseases (NAITD)(P < 0.01), respectively. Positive rate of GADA,IA-2A and ZnT8A in patients with T1DM was 34.52% (29/84), 25.00% (21/84) and 38.10% (32/84), respectively, higher than that in T2DM group (P < 0.001).In AITD group, the occurrence rate of CD (P < 0.05) and positive rate of any islet autoantibody (P < 0.05) in patients with positive TGA was higher than that of TGA negative patients. In addition, there was a positive correlation (r = 0.567, P < 0.01) between TGA and TRAb. TGA positive patients had lower body mass indexes (P < 0.05) than TGA negative patients but the rate of any islet autoantibody and age had no significant difference in T1DM group. Conclusion Serum level of TGA in patients with AITD and T1DM was elevated. Detection of TGA in patients with autoimmune diseases was very important for the early diagnosis and prevention of APS.