The cellular control switches are regulated through an extensive network of interactive intracellular signal transduction pathways, such as the mitogen-activated protein kinase (MAPK) family. The MAPK pathways may play an important role in the inappropriate inflammatory responses that lead to systemic inflammatory response syndrome or multiple organ dysfunction syndrome. Therefore, elucidating the activation status of the MAPK pathways may be a method to identify patients at risk for systemic inflammatory response syndrome/multiple organ dysfunction syndrome. Also, manipulating the proper pathways may improve patients' outcomes. However, the MAPK family is part of a complex interactive network, which may initiate an unpredictable reaction to the indiscriminate inhibition or activation of a single component. A major challenge is to elucidate the principles by which the network is assembled, so a more tissue- and temporal-specific approach can be used.