Recent studies demonstrated the development of a central, hypoxic core in incubated rat skeletal muscles. The influence of a central core on changes in protein synthesis rate, observed in incubated muscles from septic rats, is not known. In the present study, intact soleus muscles from 40 to 60-g sham-operated control rats and from septic rats (16 hours after cecal ligation and puncture) were incubated in vitro in a flaccid or stretched state. Protein synthesis rate was determined in whole muscle and in the central core and periphery of the muscle by measuring incorporation of 14C-phenylalanine into protein. Protein synthesis rate in vivo was measured with a flooding-dose technique using 3H-phenylalanine. The development of a central, hypoxic core in incubated muscles was assessed histochemically by staining the muscles for α-glucan phosphorylase activity. A central core with loss of α-glucan phosphorylase activity was noted after incubation for 30 minutes in both control and septic muscles. The protein synthesis rate was lower in the central core than in the periphery of incubated flaccid control muscles. In all other in vitro muscle preparations, however, there were no significant differences in protein synthesis rate among whole muscles, central core, and periphery. Protein synthesis rate in septic muscles was reduced to a similar extent, approximately 20%, in vivo and in the different in vitro preparations, both when measured in whole muscle and in the central core or periphery. The present results suggest that incubated soleus muscles from small rats can be used to evaluate the effect of sepsis on protein synthesis, despite the development of a central, hypoxic core in these muscle preparations.