The hallmark of a eukaryotic cell is the division of the cell contents into specialized membrane bounded compartments. These organelles provide multiple benefits to the cell, including protecting the rest of the cell from dangerous reaction products, generating gradients that can be exploited for biological processes, and separating potentially interfering pathways. Of the numerous organelles in eukaryotic cells, two provide evidence of endosymbiosis since they contain small genomes and are bounded by double instead of single membranes: the mitochondrion and the chloroplast. Their genomes encode key proteins needed for the specialized function of these organelles, including some components of a separate translation system, and a variable phalanx of other genes. In the origins of these organelles lie new possibilities for intervention in diseases caused byapicomplexan parasites, including birth defects, blindness, and encephalitis due to T. gondii, malaria due to Plasmodium species, and numerous veterinary diseases. The intense interest in the endosymbiont organelles of apicomplexans lies inthe realization that these parasites have not one but two extrachromosomal DNAs, each residing in its own organelle.