Molecular biology provides a range of tools for epidemiological investigations. So far, there has been limited application of molecular epidemiology in leishmaniasis research. The type of questions that can be addressed may be geographical or populational, may relate to the life cycle and to the disease caused. PCR-RFLPs, DNA sequencing and microsatellites have been applied. No single method has an adequate combination of discriminatory power, reproducibility and simplicity to be applied to all questions and their use will be discussed. The availability of the genome sequences for Leishmania major and Leishmania infantum will give significant impetus to the development of new tools. Multiple user databases will maximise exploitation of the new genetic markers.