The innate immune system provides sophisticated defense mechanisms to protect complex macroorganisms from the attack of microorganisms. Among those, the complement system and Toll-like receptors are of paramount importance to discriminate between infectious non-self and non-infectious self and to provide critical danger signals instructing adaptive immune responses. Here, we will discuss recent advances in our understanding of the mechanisms underlying complement and TLR-mediated regulation of adaptive immunity. We will focus on the regulation of T cell immunity and discuss recent findings on the cross-talk between complement receptor and TLR signaling pathways. Such cross-talk is likely to affect the outcome of infections with intracellular pathogens, as well as the initiation and maintenance of aberrant immune responses leading to autoimmunity and atopy.