The real time PCR technique requires the normalization of the gene of interest to reference genes that are accepted to be ubiquitously expressed. The choice of the reference gene(s) needs to be determined by researchers according to the particular tissue or model of interest. The best normalization gene is not easy to decide, particularly if the investigated tissue displays architectural changes and structural reorganization. We have investigated the expression of four housekeeping genes that are widely used for the normalization purposes (TATA binding protein, beta actin, hypoxanthine-guanine phosphorybosyl transferase and glyceraldehyde-3-phosphate dehydrogenase) in a skeletal muscle degeneration model applied by the release of the Achilles tendon which leads to a time-course degeneration of the soleus and gastrocnemius muscles. This study indicates that the TATA binding protein and the beta actin gene to be the least effected in the course of degeneration induced by tenotomy in rat soleus and gastrocnemius muscle.