Gastrointestinal parasites are important infectious causes of diarrhoea in captive non-human primates (NHP). However, prevalence data of gastrointestinal parasites in zoological gardens are scarce. Therefore, a cross-sectional survey was conducted to estimate the occurrence of gastrointestinal parasites in NHP of four zoological gardens in Belgium. Between August 2004 and April 2006, 910 faecal samples were collected from 222 animals housed in 39 groups. The 31 species involved were representatives of prosimians, New World (NW) monkeys, Old World (OW) monkeys and apes. Because individual sampling was impossible, a statistical simulation was performed to estimate a sufficient sample size. All samples were microscopically examined after an acetic acid-ether concentration. Differences in host species susceptibility were examined by non-parametric tests. Entamoeba spp. (44%) and Giardia spp. (41%) were the most prevalent species. Other parasites detected were Endolimax nana (36%), Chilomastix mesnili (21%), Balantidium coli (13%), Trichuris spp. (10%), Iodamoeba bütschlii (5%) and Strongyloides spp. (5%). Parasites for which a significant difference in susceptibility at the level of host taxonomy was noted were Entamoeba spp. (p<0.001) and C. mesnili (p<0.05). Samples containing Entamoeba spp. were the most prevalent in OW monkeys (p<0.0083). Samples collected from OW monkeys contained the highest number of parasite species (p<0.0083).