The pentraxin superfamily consists of highly conserved multimeric pattern recognition proteins, which are components of the humoral arm of innate immunity. Besides the classical pentraxins (C-reactive protein and serum amyloid P component), pentraxin 3 (PTX3) is a prototypic long pentraxin. In response to primary inflammatory signals, this multifunctional acute phase protein is produced by a variety of cell types. Recently, several clinical studies have demonstrated that PTX3 is significantly associated with kidney dysfunction and disease activity or severity in various inflammatory, cardiovascular and autoimmune diseases. In this paper, we will review the general characteristics of PTX3 focusing in particular on its fundamental biological functions in the course of acute and chronic kidney diseases.