Regular physical activity improves glucose tolerance and decreases adiposity. Our aim was to investigate the effects of exercise training on subcutaneous (inguinal) and visceral (parametrial) adipose tissue in rats that were fed a chow diet (13% fat) or made insulin resistant by a high fat diet (60% fat). Sprague Dawley rats performed four weeks of voluntary wheel running or were kept as sedentary controls. The training groups fed the chow and high fat diet achieved similar running distances (8.8 ± 1.8 and 9.3 ± 1.9 km/day respectively). Training improved oral glucose tolerance in chow fed rats and prevented the glucose intolerance that occurred in sedentary rats fed the high fat diet. In both subcutaneous and visceral adipose tissue, the high fat diet-induced increases in fat pad weight (67% and 133%, respectively), adipocyte size (20% and 43%), and cell number (36% and 65%) were completely prevented by exercise training. Cytokine mRNA expression in visceral fat did not change with exercise training. However, in subcutaneous fat, training actually increased mRNA expression of several cytokines (IL 6: 80%, p<0.05; TNF-: 100%, p<0.05; IL 1Ra: 57%, p=0.08), with no detectable increases in serum cytokine concentrations. In summary, exercise training can overcome high fat diet-induced impairments in glucose tolerance and increases in adipocyte size, cell number, and fat pad mass. Improved glucose tolerance was accompanied by an increase in cytokine gene expression in subcutaneous fat. This finding raises the possibility of a specific role of subcutaneous adipose tissue in adaptive responses to exercise training.