IA-2 (islet cell Ag 512) and IA-2 beta (phogrin/IAR) are related autoantigens associated with type 1 diabetes. To determine the critical regions for autoantibody binding and which of these autoantigens is the primary target, mutant and chimeric constructs were used to characterize Ab epitope binding in sera from 217 new onset patients with type 1 diabetes and sequential samples from 141 islet cell Ab positive first degree relatives of patients. All 22 relatives and 121 of 129 patients with IA-2/IA-2 beta Abs had reactivity to IA-2-specific epitopes. These epitopes were in the juxtamembrane region (residues 601-682) and the protein tyrosine phosphatase (PTP)-like domain of IA-2. Chimeras showed that IA-2 residues 795-889 were important for IA-2-specific Ab binding in the PTP-like domain, and mutation of IA-2 residues 877 and 911, previously indicated as relevant for phosphatase activity, also reduced Ab binding. In contrast, Ab binding to IA-2 beta was limited to its PTP-like domain, most IA-2 beta Abs recognized epitopes shared with IA-2, and only 20 patients and 2 relatives had Abs to IA-2 beta-specific epitopes. In 4 relatives, IA-2 and/or IA-2 beta Abs developed in follow-up samples. In each of these, Abs to IA-2-specific epitopes were the first detected. In three, spreading to epitopes shared between IA-2 and IA-2 beta in subsequent samples was seen. In the 17 relatives who developed type 1 diabetes, progression to disease was associated with reactivity to multiple IA-2/IA-2 beta epitopes. These data suggest that IA-2 is the primary phosphatase-like autoantigen associated with type 1 diabetes and that studying autoantibody epitope diversity may assist in disease prediction.