The innate immune system comprises a cellular and a humoral arm. The long pentraxin PTX3 is a fluid phase pattern recognition molecule, which acts as an essential component of the humoral arm of innate immunity. PTX3 has antibody-like properties including interactions with complement components. PTX3 interacts with C1q, ficolin-1 and ficolin-2 as well as mannose-binding lectin, recognition molecules in the classical and lectin complement pathways. The formation of these heterocomplexes results in cooperative pathogen recognition and complement activation. Interactions with C4b binding protein and factor H, the principal regulators of the classical, lectin and alternative complement pathways, show that PTX3 also may have a major influence on the regulation of the complement system. The complex interaction of PTX3 with the complement system at different levels has broad implications for host defence and regulation of inflammation.