During 2005, the intestinal parasitic infections in the adult HIV/AIDS patients in a combined AIDS-care centre and hospice in Thailand were identified in a cross-sectional study. Overall, 41 (45.6%) of the 90 stool samples investigated, by microscopy and/or PCR, were found parasite-positive. Cryptosporidium was the genus most commonly encountered, with 27 (30.0%) of the patients positive for Cr. hominis and four (4.4%) positive for Cr. meleagridis. Enterocytozoon bieneusi, always of genotype D, was detected in five (5.6%) of the patients while two patients (2.2%) were found infected with Blastocystis, just one patient (1.1%) was found infected with Cyclospora cayetanensis and one more (1.1%) was found positive for Isospora belli. The only helminth infection detected was opisthorchiosis and that was only seen in two (2.2%) of the subjects. Patients with stools of unusual consistency (categorized as mucous, loose-watery or watery) were more likely to be found infected with one or more species of protozoan parasite than the patients with stools of normal consistency (P=0.022). In a multivariate analysis, compared with the other subjects, the patients with stools of unusual consistency were 4.9-fold more likely to have (opportunistic) intestinal infection with parasitic protozoa (with a 95% confidence interval for the adjusted odds ratio of 1.370-17.350; P=0.014). Although there was also a trend for stools of unusual colour (red-brown, red-orange, green, black or grey) to be positively associated with intestinal parasitic infection, this was not statistically significant (P=0.658). The observation of the consistency of stools of HIV/AIDS patients could help in the presumptive diagnosis of opportunistic protozoan infections and allow parasitological investigation to be targeted at the cases most likely to be found positive.