Avian coccidiosis, a major parasitic disease of poultry, is caused by Eimeria spp. infection. It inflicts severe economic losses on the poultry industry worldwide. To further understand the molecular basis of sporulation and invasion of Eimeria spp., suppression subtractive hybridization and microarray approaches were combined to identify novel and important genes involved in the development and invasion of the early stages of Eimeria tenella. Three subtractive cDNA libraries were constructed for 3 stages of E. tenella including unsporulated oocysts, sporulated oocysts, and sporozoites. A subset of clones was selected from the 3 subtractive libraries to construct cDNA microarrays. Microarray analysis was used to assay expression changes of these clones. A total of 657 valid expressed sequence tags (ESTs) was obtained, including 119 unique sequences, 31 from sporulated oocysts and 88 from sporozoites. Homology searches of the public sequence databases showed that, among the 119 ESTs, 32 genes encoded proteins homologous with previously reported proteins including microneme proteins and surface antigen proteins of E. tenella, small heat shock proteins, rhoptry proteins of Toxoplasma gondii, and calcium-dependent protein kinase of Plasmodium spp. Thus, the remaining 87 ESTs have not previously been reported. Further characterization of these differentially expressed genes will be useful in understanding those responsible for sporulation, invasion, growth, and development of E. tenella.