While disease and outbreaks are mainly clonal for bacteria and other asexually reproducing organisms, sexual reproduction in schistosomes and other helminths usually results in unique individuals. For sexually reproducing organisms, the traits conserved in clones will instead be conserved in the group of organisms that tends to breed together, the population. While the same tools are applied to characterize DNA, how results are interpreted can be quite different at times (see Part 4 this series). It is difficult to know what the real effect of any control program has on the parasite population without assessing the health of this population, how they respond to the control measure and how they recover, if they recover. This part of the series "Advances in Molecular Epidemiology of Infectious Diseases" will concentrate on one approach using pooled samples to study schistosome populations and show how this and other approaches have contributed to our understanding of this parasite family's biology and epidemiology. Biology of schistosomes Schistosomiasis is a spectrum of conditions caused by infection with helminthic parasites of the genus Schistosoma. There are seven species that infect humans and three of these are responsible for the bulk of disease: S. mansoni, S. haematobium and S. japonicum. S. mansoni is present in the Americas and much of Africa. S. haematobium is found in Africa and parts of the Middle East, while S. japonicum is transmitted in East Asia. More than 200 million people are infected with one or more of these species, and large outbreaks, even epidemics have occurred in association with major water resource development projects (1). The complex biology of schistosomes distributes their development between a snail host specific to each species of parasite and humans. Other mammalian species may also be infected and maintain transmission, but are generally of less importance with the exception of S. japonicum. A number of domestic and wild animals may be major reservoirs for S. japonicum. The adult parasites inhabit the vascular system where females reside within a groove formed by the male's body to produce 300-3000 eggs per day. Infection produces morbidity by the immune reaction to eggs swept along with the flow of blood back into the liver (S. mansoni and S. japonicum), in the wall of the colon or the urinary system (S. haematobium). Intensity and duration of infection along with host predisposition result in portal hypertension with esophageal varices and bleeding (S. mansoni, S. japonicum) or