The enzyme tissue transglutaminase (tTG) has been recently identified to represent a highly sensitive and specific target of autoantibodies in coeliac disease. To characterize autoantigenic epitopes, we generated novel tTG deletion mutants by polymerase chain reaction, produced radiolabelled fragments by in vitro transcription/translation, immunoprecipitated the mutants using sera from patients with coeliac disease, and related the binding data with putative structural and functional domains of human tTG. We show that tTG antibody positive sera display a heterogeneous autoantibody response covering distinct regions of the molecule. The N-terminal and C-terminal third of tTG, comprising amino acid (aa) 1–281 and aa 473–687, harbour the dominant epitopes (67·4% and 69·4% positive), whereas the catalytic region is of minor antigenicity (22·5% positive). Autoantibodies directed to one, two and three domains were observed in 36·7%, 28·6% and 22·4% of patients, respectively. Comparative analysis revealed the presence of strictly conformational epitopes which were dependent on the N-terminus (aa 1–12) or the intact β-barrel domains in the C-terminus (aa 473–497, aa 649–687). In conclusion, we here demonstrate for the first time that the humoral autoimmunity is directed against distinct functional tTG domains. The spectrum of autoantibodies indicates that the native folded protein may be the target of autoantibodies.