To protect against infectious diseases, our immune system needs to mount a rapid and robust response to microbial invasion. Innate immune activation provides the first line of defence and directs the development of adaptive responses. In mice and humans, the deleterious effects of genetic ablation of TLRs and associated signaling underpin the pivotal role of innate recognition for host protection. On the other hand, the Yin and Yang of host responses to infection and tissue damage is increasingly recognized: overshooting or prolonged activation of host effector mechanisms causes acute shock and chronic immunopathology and tissue destruction. A substantial burden of disease is due to septic shock, inflammatory bowel disease and multiple sclerosis. The question how valuable immune responses may be hindered from becoming deleterious has therefore moved to the center stage of research. Nature’s solution to this problem is the development of a multitude of endogenous negative regulatory factors and mechanisms that act on overlapping yet distinct control points. Consequently, while they all contribute to the termination of innate immune responses, dissecting the effects of negative regulators at the level of signal transduction, cytokine gene expression and mediator release may answer the question how specific pathways of innate immune responses can be manipulated to tip the balance in the desired direction. The advent of functional genomics methods like genome-wide transcriptome analysis has enabled us to investigate the full spectrum of transcriptional responses to infectious danger at the level of individual cells as well as tissues. The combination of gene expression profiling with genetically defined mouse models has proven particularly useful for the definition of pathway-specific signatures. Examples of this approach for the elucidation of activating signaling pathways and negative regulatory mechanisms in models of infection and inflammation will be presented.