Islet-level oxidative stress has been proposed as a trigger for Type 1 diabetes (T1D) and release of cytokines by infiltrating immune cells further elevates reactive oxygen species (ROS), exacerbating beta cell duress. To identify genes/mechanisms involved with diabetogenesis at the beta cell level, gene expression profiling and targeted follow-up studies were used to investigate islet activity in the BioBreeding (BB) rat. Forty day-old spontaneously diabetic lymphopenic BB DRlyp/lyp rats (prior to T cell insulitis), as well as nondiabetic BB DR+/+ rats, nondiabetic but lymphopenic F344lyp/lyp rats, and healthy Fischer (F344) rats were examined. Gene expression profiles of BB rat islets were highly distinct from F344 islets and under-expressed numerous genes involved in ROS metabolism, including glutathione S-transferase (GST) family members (Gstm2, Gstm4, Gstm7, Gstt1, Gstp1 and Gstk1), super-oxide dismutases (Sod2, Sod3), peroxidases, and perioxiredoxins. This pattern of under-expression was not observed in brain, liver or muscle. Compared to F344 rats, BB rat pancreata exhibited lower GST protein levels, while plasma GST activity was found significantly lower in BB rats. Systemic administration of the antioxidant N-acetyl cysteine to DRlyp/lyp rats altered abundances of peripheral eosinophils, reduced severity of insulitis, and significantly delayed but did not prevent diabetes onset. We find evidence of beta cell dysfunction in BB rats independent of T1D progression which includes lower expression of genes related to anti-oxidative defense mechanisms during the pre-onset period that may contribute to overall T1D susceptibility.