Over the past 5 years, our knowledge about how the immune system senses the microbial world has changed fundamentally. It has been known for decades that microbial products such as lipopolysaccharide or bacterial DNA have a profound activity on human cells. Whereas the molecular structure of many different pathogenic microbial compounds has been extensively studied and characterized, the molecular basis of their recognition by the immune system remained elusive for a long time. It was the late Charles Janeway who developed the idea of microbial structures forming pathogen-associated molecular patterns (PAMP) that would be recognized by pattern-recognition receptors [1]. Even if the notion of pattern recognition is challenged today, the discovery of the family of Toll receptors in species as diverse as Drosophila and humans, and the identification of their role in distinguishing molecules and structures that are common to microorganisms has led to a renewed appreciation of the innate immune system. This review focuses on the current knowledge about the different molecules that are recognized by Toll receptors in mammalian cells.