Chronic reductions in muscle activation and loading are associated with decreased heat shock protein 25 (Hsp25) expression and phosphorylation (pHsp25) which, in turn, may contribute to elevated caspase-3-mediated muscle protein breakdown. Thus, the purpose of the present study was to determine whether there are any changes in Hsp25, pHsp25 and caspase-3 activity among rat muscles having different fibre type compositions and functions [soleus, adductor longus (AL), plantaris and tibialis anterior (TA)] at 0 (control), 1, 8 or 28 days after a complete spinal cord transection (ST). The Hsp25 levels were unaffected on days 1 and 8 in all muscles, except for a significant reduction on day 8 in plantaris. The Hsp25 levels were lower than control values in all muscles except TA on day 28. The pHsp25 levels were lower than control values after 8 and 28 days in plantaris and AL and after 28 days in soleus, but higher than control in TA after 8 and 28 days. Caspase-3 activity was higher in ST than control rats on day 8 in all muscles except TA. Caspase-3 activity was negatively correlated with muscle mass for all muscles. In plantaris, Hsp25 and pHsp25 were negatively correlated with caspase-3 activity and Hsp25 was correlated with muscle mass. These relationships were not observed in other muscles. Thus, the effects of ST on Hsp25 and caspase-3 are muscle specific and time dependent, factors that should be considered in developing any intervention to maintain muscle mass after a spinal cord injury.