Antigen-presenting cells, such as macrophages and dendritic cells, represent a central and important part of the immune defence against invading microorganisms, as they participate in initial capture and processing of microbial antigens (innate immunity) and then activation of specific T and B cell effector mechanisms (acquired immunity). Recognition of microbial molecules by antigen-presenting cells occurs through so called pattern recognition receptors (PRRs), which recognize conserved structures, or pathogen-associated molecular patterns, in pathogenic microbes. The Toll-like receptors are the most extensively studied of these receptors, but accumulating evidence shows that other PRRs, such as scavenger receptors, C-type lectin receptors and NOD-like receptors, also play important roles in the innate immune defence. Here, we summarize current knowledge of the role of various PRRs in the defence against pathogenic microorganisms and we report recent advances in studies of different receptor-ligand interactions. In particular, we focus on the importance of microbial proteins as ligands for PRRs.