This chapter provides a short review of the immune system of urochordates, the closest living relative of vertebrates. Since adaptive immunity is a unique property of vertebrates, urochordates rely exclusively on innate immunity to recognize and eliminate pathogens. Here we discuss three immune systems of urochordates which show different evolutionary relationship with the vertebrate immune system. Urochordate Toll-like receptors (TLR) show a clear orthologous relationship with vertebrate counterparts, although they show unique characteristics most likely gained in the urochordate lineage. The urochordate complement system also shows orthologous relationship with the vertebrate complement system. From the structural and functional viewpoints, it seems to represent a more primitive state ofthe vertebrate complement system without any major deviation. In contrast, the allorecognition systems of urochordates show no evolutionary relationship with any invertebrate or vertebrate systems, suggesting that they were invented in the urochordate lineage.