In the world there are around 95% animal species that are the invertebrates which have to get rid of with various pathogens like bacteria, fungi, viruses and parasites with innate immune system. In contrast to vertebrates, that possess an adaptive as well as an innate immunity, the invertebrates have an efficient innate system based on fast response to an infection. A wide variety of immune proteins, such as pattern recognition receptors (PRRs), antimicrobial peptides (AMPs), immune signaling molecules, and enzymes, mediate invertebrate immunity. The Protein Data Bank (PDB), a useful and significant repository of three-dimensional structures of macromolecules (Berman et al., 2000), has been a key source from which immune proteins are being extracted. We emphasize structural characteristics and functions of the immune proteins from different invertebrate phyla, from the point of view of structure and function as pathogen recognition and defense molecules or as immune activation triggers, using data available on the PDB.