In a 12-month longitudinal study, a cohort of Mexican HIV+/AIDS patients was checked several times for Entamoeba infection, with the parasites identified, as E. histolytica or E. dispar, using PCR. The polymorphic region of the parasites' chitinase genes was investigated by PCR, with the variation in amplicon sizes being used as a measure of the genetic variation among the isolates. The patients found infected with Entamoeba at the start of the study displayed varied patterns of infection clearance and re-infection. The analysis of the polymorphisms in the chitinase gene revealed seven polymorphic patterns in the E. histolytica isolates investigated and three in the E. dispar isolates. Many of the patients were each re-infected with Entamoeba at least once during the 12 months of follow-up. As seen in a previous study in Mexico, none of the E. histolytica-infected patients developed any clinical symptoms of invasive amoebiasis during the follow-up period. The results highlight the complexity of the host-parasite relationship in human amoebiasis.