In the first decade of the 21st century, we have witnessed the development of new technologies that have forever changed the way genomes are sequenced. Combined with high-throughput applications of established Sanger capillary electrophoresis, Next Generation Sequencing (NGS) is revolutionizing how parasite genomes are decoded and interrogated due to extraordinary increases in speed and decreased cost. The concurrent development and application of tools to characterise the function of these parasite genomes complements the generation of sequence data. Indeed, such tools are collectively responsible for many of today?s novel parasite biological discoveries. Thus, it is the intention of this special edition of Parasite Immunology to highlight recent advances in the fields of parasite genomics and post-genomic activities as they apply to both protozoan (within the Apicomplexa, the Amoebozoa and the Euglenozoa) and metazoan (within the Nematoda and Platyhelminthes) pathogens. As guest editors, we have solicited eleven contributions from experts within the Parasitology community and have specifically asked the authors to provide reviews, updates or perspectives that illustrate how next generation genomics is rapidly shaping inter-disciplinary science. We believe that these contributions provide a robust resource for the parasite immunologist interested in discovering how parasite genome information and post-genomic activities can help shape immunological-driven investigations of host/parasite interrelationships. We contend that integration of disciplines in this manner will play a major role in the future control of these biomedically relevant parasites.