To elucidate the genetic factors contributing to heterogeneity of the rate of -cell destruction in type 1 diabetes, we investigated the relationship between the time course of complete -cell loss and HLA class I and II alleles. HLA allele frequencies were also examined among subgroups classified by the mode of onset. The subjects were 266 type 1 diabetic patients (among whom 196 patients were studied longitudinally) and 136 normal control subjects. Earlier complete loss of -cell function was observed in patients who possessed both HLA-A24 and HLA-DQA1*03 and in patients who had HLA-DR9, compared with those without these HLA alleles (P ؍ 0.0057 and 0.0093, respectively). Much earlier complete -cell loss was observed in the patients who possessed all of HLA-A24, -DQA1*03, and -DR9 compared with the remaining patients (P ؍ 0.0011). The combination of HLA-A24, -DQA1*03, and -DR9 showed a higher frequency in acute-onset than slow-onset type 1 diabetes (P ؍ 0.0002). In contrast, HLA-DR2 was associated with a slower rate of progression to complete -cell loss. These results indicate that the combination of HLA-A24, -DQA1*03, and -DR9 contributes to the acute-onset and early complete -cell destruction, whereas HLA-DR2 has a protective effect against complete -cell loss in type 1 diabetes.