Abstract Background: Type 1 diabetes mellitus (DM1) can cause damage to several physiological systems. Objectives: To compare and characterize the effects of aerobic exercise training (ET) performed by swimming with those of ET performed on a treadmill on the skeletal muscle and heart of rats with DM1. Methods: 41 male Wistar rats were randomized into four groups: nondiabetic control (CTR), diabetic control (DMC), diabetic trained on the treadmill (DMT), and diabetic trained by swimming (DMS). The trained groups performed aerobic exercise training for 8 weeks, 5 times a week, 60 min per day. Exercise tolerance, blood glucose, body weight, wet weight of the skeletal muscles and left ventricle (LV), muscle glycogen, cross-sectional area of skeletal muscles, and cross-sectional diameter and collagen volume fraction of the LV were evaluated. Results: The results were expressed as mean ± standard deviation of the mean and submitted to two-way ANOVA with post-hoc Bonferroni test. Aerobic ET protocols applied to animals with DM1, regardless of the ergometer, showed satisfactory results (p < 0.05) when compared to the control groups: improved exercise tolerance, increased glycogen content of the soleus and extensor digitorum longus (EDL) muscles and increased cross-sectional diameter of the left ventricular cardiomyocytes. In some variables, such as exercise tolerance and cross-sectional area of the soleus and EDL muscles, DMT showed better results than DMS (p < 0.05). On the other hand, DMS showed increased cross-sectional diameter of cardiomyocytes when compared with the DMT group. Conclusion: Both aerobic ET protocols offered benefits to animals with diabetes; however, due to the specific characteristics of each modality, different physiological adaptations were observed between the trained groups.