Sensing of nucleic acids by innate immune pathways is essential for normal immunity against viruses, and defects in this process lead to autoimmune diseases. Cleavage of intracellular DNA is mediated by molecules of the SET complex, and this complex can be activated by the serine protease granzyme A. Mutations in molecules in the SET complex, such as the 3’ exonuclease Trex1, result in autoimmunity in mice and man that is driven by excessive production of type I interferon (IFN). While studying cytotoxic T cell-mediated pancreatic beta cell death in type 1 diabetes (T1D), we discovered that non-obese diabetic (NOD) mice lacking granzyme A (NOD.Gzma-/-) have accelerated diabetes. NOD.Gzma-/- mice had more islet autoantigen-specific T cells in the pancreatic lymph nodes and islets than wild-type NOD mice. Further investigation revealed islets from granzyme A-deficient NOD mice had a 3- to 6-fold increase in the expression of IFN-response genes including Mx1, Ifit1, Isg15 and Oas1a between 2-6 weeks of age compared to wild-type NOD mice, indicating excessive activation of innate immunity and type I IFN production. Single-stranded DNA was observed more frequently in the cytoplasm of immune cells infiltrating the islets in NOD.Gzma-/- mice than in NOD mice at 4 and 10 weeks of age, suggesting that cleavage of aberrant DNA is less efficient in NOD.Gzma-/- mice. Our data indicate a crucial role for granzyme A in controlling activation of innate immunity, and if left unchecked in a genetic background that is prone to autoimmunity, disease develops.