Abstract Background Diabetic nephropathy and liver damage are important complications of diabetes mellitus (DM). Various factors, such as sirtuins (silent information regulators or SIRTs) are associated with these complications. Sirtuins are a family of NAD⁺-dependent proteins, and seven types of these can be found in mammalians. In this study, we evaluated the effects of aqueous garlic extract (G) on the expressions of SIRT1 and SIRT2 genes in the kidney and liver tissues of rats with types 1 and 2 diabetes. Methods A total of 36 male Wistar rats (230–280 g) were randomly divided into six groups: C: normal control rats, D1M: type 1 diabetic rats (induced with streptozotocin, STZ), D1M+G: type 1 diabetic rats that treated with garlic extract, D2M: type 2 diabetic rats (induced with STZ and niacinamide), D2M+G: type 2 diabetic rats treated with garlic extract, and G: normal rats that received garlic extract. At the end of the treatment time, kidney and liver tissue samples were collected from all rats. The SIRT1 and SIRT2 gene expressions were determined by qRT-PCR. Results The SIRT1 and SIRT2 gene expressions in the liver and kidney tissues of diabetic rats decreased significantly compared with those in the control rats (p<0.05). After treatment with garlic extract, the gene expressions also increased significantly compared with those in the diabetic rats and are close to normal level (p<0.05). Conclusions Garlic extract increased the SIRT1 and SIRT2 gene expressions in the livers and kidneys of diabetic rats. The antioxidant and anti-inflammatory effects of garlic have been proven in many studies. Thus, it is possible that garlic – with its effects on this pathway of gene expression – can have antioxidant and anti-inflammatory effects, thus decreasing diabetic complications.