AimsTo investigate if HLA risk haplotypes and HbA1c levels are associated with the expression levels of innate anti‐viral immune pathway genes in type 1 diabetes.Materials and MethodsWe investigated RNA expression levels of innate anti‐viral immune pathway genes in laser‐dissected islets from two to five tissue sections per donor from the Diabetes Virus Detection study and the network of Pancreatic Organ Donors in relation to HLA risk haplotypes (non‐predisposed and predisposed) and HbA1c levels (normal, elevated, and high).ResultsThe expression of innate anti‐viral immune genes (TLR7, OAS1, OAS3 etc.) was significantly increased in individuals with predisposing vs non‐predisposing HLA haplotypes. Also, the expression of several of the innate anti‐viral immune genes from the HLA risk haplotype analysis was significantly increased in the group with high vs normal HbA1c. Furthermore, the gene expression of OAS2 was significantly increased in the group with high HbA1c vs elevated HbA1c.ConclusionsExpression of innate anti‐viral immune pathway genes was increased in individuals with predisposing HLA risk haplotypes and those with high HbA1c. This indicates that type 1 diabetes might well begin with alterations in innate anti‐viral immunity, and already at this stage be associated with HLA risk haplotypes.