Over the past several decades a great deal of effort has been invested in developing new control and vaccination strategies for apicomplexan protozoan parasites. These organisms are the cause of some of the most significant and harmful diseases in both humans and animals worldwide and include as examples; Plasmodium (malaria) and Cryptosporidium in humans, Toxoplasma in humans and animals, Babesia and Neospora in cattle, and Eimeria the cause of coccidiosis in animals (poultry, sheep, cattle, etc.). In spite of a great deal of progress made in understanding at the molecular level how these organisms invade, survive and transmit in their respective hosts, there has been a paucity of new vaccines commercially developed against these parasitic protozoa over the past few decades. In this chapter, we will discuss the types of strategies being developed to help control these parasites, which includes the development of live and subunit (both native and recombinant DNA based) vaccines, the search for and use of new or existing drugs (such as artemisinin combination therapy against malaria), as well as simpler management & hygiene strategies that can be employed to help alleviate the burden of parasitic diseases