Sepsis is a complex pathophysiological disorder arising from a systemic inflammatory response to infection. Patients are clinically classified according to the presence of signs of inflammation alone, multiple organ failure (MOF), or organ failure plus hypotension (septic shock). The organ damage that occurs in MOF is not a direct effect of the pathogen itself, but rather of the dysregulated inflammatory response of the patient. Although mechanisms underlying MOF are not completely understood, a disruption in cellular energetic metabolism is increasingly implicated. In this review, we describe how various factors affecting cellular ATP supply and demand appear to be altered in sepsis, and how these vary through the timecourse. We will emphasise the need for an integrated systems approach to determine the relative importance of these factors in both the failure and recovery of different organs. A modular framework is proposed that can be used to assess the control hierarchy of cellular energetics in this complex pathophysiological condition.