InnateDB is one of the first databases and integrated analysis platforms specifically designed to facilitate systems-level analyses of the mammalian innate immune response. First published in Molecular Systems Biology in 2008, InnateDB has grown since then and now has more than 10,000 users annually world-wide. InnateDB includes over 20,000 manually curated molecular interactions of relevance to innate immunity, providing unprecedented insight into innate immunity networks and pathways and their component molecules.