Different studies have illustrated the activation of the innate immune system during infection with protozoan parasites. Experiments performed in vivo also support the notion that innate immunity has a crucial role in resistance as well as pathogenesis observed during protozoan infections such as malaria, leishmaniasis, toxoplasmosis, and trypanosomiasis. While major advances have been made in the assignment of bacterial molecules as Toll-like receptors (TLRs) agonists as well as defining the role of the Toll/interleukin-1 receptor (TIR) signaling pathway in host resistance to bacterial infection, this research area is now emerging in the field of protozoan parasites. In this review, we discuss the recent studies describing parasite molecules as TLR agonists and those studies indicating the essential role of the TIR-domain bearing molecule named myeloid differentiation factor 88 in host resistance to infection with protozoan parasites. Together, these studies support the hypothesis that the TIR signaling pathway is involved in the initial recognition of protozoan parasites by the immune system of the vertebrate host, early resistance to infection, development of acquired immunity, as well as pathology observed during acute infection with this class of pathogens.