Understanding the pathogenesis of infectious diseases requires comprehensive knowledge of the proteins expressed by the pathogen during in vivo growth in the host. Proteomics provides the tools for such analyses but the protocols required to purify sufficient quantities of the pathogen from the host organism are currently lacking. In this study, we have separated Clostridium perfringens, a highly virulent bacterium and potential BTW agent, from the peritoneal fluid of infected mice using Percoll density gradient centrifugation. The bacterium could be isolated in quantities sufficient to carry out meaningful proteomic comparisons with in vitro grown bacteria. Furthermore, the isolates were found to be virtually free from contaminating host proteins. Microscopy revealed major morphological changes under host conditions at different stages of infection. Profile of immunogenic proteins from in vivo- and TPYG-grown whole cell lysate using mouse anti-gangrene serum indicated over-expression of several proteins especially in the low molecular weight region. Expression of two virulence determinants, ornithine carbamoyl transferase (cOTC), and cystathionine beta-lyase (CBL), under in vivo conditions has also been studied. Two-dimensional gel analysis revealed a host induced proteome which was apparently different in comparison to in vitro grown cells. Detailed proteomic elucidation of differentially expressed proteins shown here is likely to provide valuable insight towards understanding the complexity of the adaptive response of C. perfringens to the host environment.