The purpose of the present study was to evaluate the role of exercise training on the development of papain-induced emphysema in rats. Our hypothesis was that the increase in pulmonary tissue stretching associated with exercise could increase the severity of a protease-induced emphysema. Wistar rats were randomly assigned to four groups (n = 10 for each group) that received, respectively, intratracheal infusion of papain (6 mg in 1 ml NaCl 0.9%) or vehicle and were submitted or not to a protocol of exercise on a treadmill. Rats exercised at 13.3 m/min, 6 days per week, for 9 weeks (increasing exercise time, from 10 to 35 min). We measured respiratory system elastance (Ers) and resistance (Rrs), the size and weight of the heart and pulmonary mean linear intercept (Lm). After 9 weeks of exercise training, there were no differences in Rrs and Ers values among the four experimental groups. Volume of the heart was significantly greater in rats submitted to exercise training (P = 0.007) compared to sedentary rats, due to increases in volumes of both right and left cardiac chambers. Lm was significantly greater in rats that received papain compared to saline-infused rats (P = 0.025). Surprisingly, this was true even though there was no significant decrease in elastance, possibly due to connective tissue remodeling. However, Lm was significantly greater in papain + exercise rats compared to rats that received papain and were not submitted to exercise. We conclude that exercise training can increase alveolar damage induced by papain infusion.