This critical care perspective appraises reprogramming of gene expression in inflammatory diseases as an emerging concept of clinical importance. We emphasize gene reprogramming that 'silences' acute proinflammatory genes during severe systemic inflammation, wherein in the systemic inflammatory response syndrome (SIRS) exists as a continuum during severe sepsis, septic shock and the multiorgan dysfunction and failure phenotypes without infection In contrast, silencing of acute proinflammatory genes is not apparent in sites of localized inflammatory processes like rheumatoid arthritis. We discuss in three parts the clinical context and the translational basic science associated with gene silencing during the SIRS continuum of severe systemic inflammation: 1) reprogramming of acute proinflammatory genes; 2) an 'NF-BB paradox', coupled with RelB expression that combine to silence genes using an epigenetic (inherited and reversible) signature on the nucleosome; and 3) the potential clinical importance of compartmentalization in gene silencing. Our emergent understanding of these physiological processes may provide a novel framework developing treatments.