To seek unknown molecules and pathways that might be responsible for the pathogenicity of ruminant coccidiosis, the protein expression profiles of Eimeria bovis and Eimeria alabamensis were compared by 2-dimensional gel electrophoresis. The average gel of E. bovis contained 938 ± 132 protein spots having an experimental isoelectric point (pI) range of 4.58 to 7.95 and a mass range of 19.1 to 138.2 kDa. A total of 692 ± 129 protein spots with pIs ranging from 4.39 to 7.84 and masses between 17.6 and 127.8 kDa were included in the average gel of E. alabamensis. Our results provide a valuable starting point to detect differences in protein expression distribution between 2 Eimeria species that cause cattle coccidiosis and may also serve as a useful tool for further investigation of the basis accounting for their sharp difference in virulence.