Metformin is an adjuvant drug used in the treatment of obesity and diabetes, two conditions associated with stress and chronic inflammation that affects thymus structure and function.Recent evidence suggests a complex role of metformin in thymic homeostasis. The study was designed to develop an animal model of obesity and type 2 diabetes, and treat it with metformin to evaluate its effects on the thymus. In addition, its general effects on body weight and blood glucose level were also investigated. Over a period of 6 weeks, 30 albino male mice (4-5 weeks) were fed either regular chow (control group, N=10) or high fat diet (obese group). The obese group was then subjected to low dose streptozotocin induction of diabetes and divided into two subgroups, one of which was treated with metformin (N=10) while the other was not (N=10). Body weight, random blood sugar, relative thymus weight were recorded. Thymic tissue sections were stained with H & E to study general histology and with single immunohistochemical stain to detect regulatory T-cell using FOXP3 marker. Thymic corticomedullary ratio and regulator cell frequency were calculated. Metformin was successful in reducing body weight and blood glucose levels in treated animals. The thymus had higher relative weight and less cortical cellularity but more frequently counted regulatory cells.Untreated animals showed signs of thymic involution but increased corticomedullary ration in response to reduced regulator cell counts. Metformin has both direct and indirect effects in correcting metabolic abnormalities associated with obesity and diabetes. These effects are anti-inflammatory and may be responsible for stimulation of thymic immunosuppressive cells.Contrariwise, obesity and diabetes have detrimental effects on thymus structure and homeostasis.