During chronic obstructive pulmonary disease (COPD) diaphragm and peripheral muscle weakness occur. Muscle remodeling and wasting may be a result of apoptosis and changes in muscle specific transcription factors, such as MyoD, altering muscle specific gene transcription and muscle regenerative capacity. To investigate this we instilled under ketamine/xylazine anesthesia porcine elastase in the lungs of hamsters to induce emphysema. The emphysematous hamster is an accepted model for COPD. In the diaphragm and peripheral muscles we assessed the occurrence of apoptosis, and in the diaphragm and soleus also the expression of MyoD and inhibitor of differentiation protein 2 (Id2). There was no significant muscle atrophy in emphysematous hamsters. The mRNA levels of tumor necrosis factor- (TNF) and markers of apoptosis were significantly elevated in the diaphragm and soleus muscles during emphysema. This was accompanied by an increased presence of nucleosomes in the cytosol. Caspase 3 activity and the DNA-binding activity of the p65 sub-unit of NF-B, however, were unaltered in all muscles. The protein expression of MyoD and Id2 were decreased and increased respectively in the diaphragm and the soleus muscle. Thus, despite the absence of muscle atrophy in emphysematous hamsters, there was evidence of increased TNF expression, apoptosis and altered muscle specific transcriptional regulation as reflected by decreased MyoD and elevated Id2 levels at least in the soleus and diaphragm muscle. These alterations may impair the regenerative capacity of skeletal muscles and ultimately contribute to muscle wasting.