DNA microarray analysis has been successfully applied to most of the protozoan parasites that cause human disease, but has not made equal progress in all cases. The results for kinetoplastid parasites (Leishmania and Trypanosoma) are primarily at the stage of validation and new gene discovery. By contrast, the results for apicomplexan parasites (Plasmodium and Toxoplasma) have advanced to the analysis of coordinate regulation of clusters of genes. This difference in progress relates to the more complete genome sequence identified for the apicomplexans and, more significantly, to the differences in the regulation of gene expression between these two groups.