Coccidiosis is a ubiquitous intestinal protozoan infection of poultry seriously impairing the growth and feed utilization of infected animals. Conventional disease control strategies have relied on prophylactic medication. Due to the continual emergence of drug resistant parasites in the field and increasing incidence of broiler condemnations due to coccidia, novel approaches are urgently needed to reduce economic losses. Understanding the basic biology of host-parasite interactions and protective intestinal immune mechanisms, as well as characterization of host and parasite genes and proteins involved in eliciting protective host responses are crucial for the development of new control strategy. This review will highlight recent developments in coccidiosis research with special emphasis on the utilization of cutting edge techniques in molecular/cell biology, immunology, and functional genomics in coccidia vaccine development. The information will enhance our understanding of host-parasite biology, mucosal immunology, and host and parasite genomics in the development of a practical and effective control strategy against Eimeria and design of nutritional interventions to maximize growth under the stress caused by vaccination or infection. Furthermore, successful identification of quantitative economic traits associated with disease resistance to coccidiosis will provide poultry breeders with a novel selection strategy for development of genetically stable, coccidiosis-resistant chickens, thereby increasing the production efficiency.