Neurocysticercosis is a major zoonotic larval cestode infection that has a worldwide distribution and is of significant public health importance. Knowledge of the genetic structure of Taenia solium can be applied to the epidemiology and transmission of this disease, since genetic variants may differ in infectivity and pathogenicity. Molecular epidemiological approaches can also enable detailed studies of transmission. On a global scale, mitochondrial markers have differentiated between T. solium isolates from Asia and isolates from Africa/Latin America. Intraspecific variation in T. solium has been detected to some extent, using RAPD markers to differentiate between T. solium populations from different regions within Mexico. Markers currently available for T. solium have not been used to analyse genetic variation at the community or local level. The development of highly polymorphic markers such as microsatellites in T. solium can provide the means to examine genetic heterogeneity of tapeworm infection at the household, community and regional level. Preliminary studies suggest it is possible to analyse population genetic variation in communities using a range of polymorphic markers. © 2005 Elsevier Ireland Ltd. All rights reserved.