Many fundamental aspects of the biology of Eimeria spp. from the chicken remain poorly understood and some have not been investigated in detail for many years. New molecular tools are now available that could be used to underpin some of the more practical aspects of disease control. For example, a far better understanding of the epizootiology of the parasites, with precise knowledge of the characteristics of individual species and strains that are prevalent in the field might, in the future, be incorporated into strategies that see a more rational use of the available drugs and vaccines. The recent use of electrophoretic variation of enzymes to investigate parasite epizootiology is described and the general case for the development of specific, more sensitive DNA-based technologies is discussed. A wealth of DNA probes is potentially available from the large genome of Eimeria spp. and the genetic complexity of these parasites has recently been illustrated in more detail. In addition to a large nuclear genome comprising at least 14 linear chromosomes, studies on E. tenella have shown that, like Plasmodium and Toxoplasma, it also possesses a mitochondrial genome and a newly discovered "plant-like" genome that probably resides within an uncharacterised organelle and was acquired when an ancestor engulfed and kept and algal cell containing a chloroplast. A double-stranded RNA genome has also been identified in some species.