With the Eimeria spp. populations that infect chickens used as a model for coccidian biology, we aimed to survey the transcriptome of Eimeria maxima and contrast it to the 2 other Eimeria spp. for which transcriptome data are available, i.e., Eimeria tenella and Eimeria acervulina. The asexual intracellular development stage, the merozoite, was specifically examined, and we used expressed sequence tag (EST) analysis to provide experimental evidence of transcription and a framework for understanding the merozoite stage of E. maxima. Of 2,680 individual ESTs obtained, 48.2% shared most significant (E < 10⁻⁵) homology to sequences from other apicomplexan species, primarily other Eimeria spp. and Toxoplasma gondii, and 47.5% were unique. Annotation of these ESTs enabled categorization to putative biological function and revealed an emphasis on translation, cytoskeleton, metabolism, signaling, transport, and protein folding, as well as the apicomplexan specific surface antigens and micronemes. Comparative analysis of abundantly expressed transcripts from merozoites of the 3 Eimeria spp. revealed a novel transcript common to all 3. Sharing no significant homology to any other sequence in public databases, this transcript was predicted to encode an Eimeria-specific protein (ESP) with 166–178 amino acids and 58.9–65.1% interspecific identity. A predicted signal peptide was identified, consistent with the assumption that ESP is a secreted protein. These annotated ESTs from E. maxima merozoites provide a resource for intra- and interspecific comparative analyses that will be useful in distinguishing the unique biology of coccidian parasites in relation to the diverse phylum of Apicomplexa.