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Objective: To test, in AIDS patients, a previously proposed hypothesis of clonal population structure in Leishmania infantum, the agent of visceral leishmaniasis. Design: Forty-three stocks of L. infantum isolated from AIDS patients in Spain were analysed by multilocus enzyme electrophoresis. Methods: The results were analysed in terms of population genetics according to previously described statistical methods. Departures from panmixia were examined by linkage disequilibrium analysis. Results: As previously shown in HIV-negative patients, classical manifestations of clonality were shown, namely strong linkage disequilibrium, over-representation of genotypes and overall lack of genotype diversity. The same dominant clonal genotype (MON1) was recorded in both HIV-positive and HIV-negative patients. Frequency of this dominant genotype was not statistically different in HIV-positive and HIV-negative patients. Conclusions: The parasite population under survey appears to be clonal parasite genotypes can therefore be equated to natural clones, stable in space and time, which can be used as multilocus epidemiological markers. Nevertheless, additional studies are required to better estimate the long-term stability of these clonal genotypes and the possible interference of gene exchange at an evolutionary scale.