Coccidiosis of domestic fowl is a worldwide disease caused by obligatory intracellular protozoa of the genus Eimeria. It is responsible for important economic losses in poultry farms. The identification of different species of Eimeria are principal for the prevention and control of coccidiosis. However, the development of vaccine against avian coccidiosis need the understanding of intestinal and systemic immune response. So, detection of Eimeria species that affect poultry farms using polymerase chain reaction (PCR) as a convenient technique than traditional method in the precise identification of Eimeria species even with non intact oocysts, and to overcome the overlapping of oocysts size among Eimeria species. Also, we develop a simple and reliable method for measurement of the local mucosal immune response by ELISA from faecal extract of the infected birds.