Stool specimens were collected from 180 patients belonging to a population of recently settled Bedouins in Jordan who presented with acute or persistent diarrhoea and other symptoms, and from 100 non-diarrhoeal controls. All samples were examined for parasites and bacterial pathogens by culture and PCR. Bacterial isolates were tested for their susceptibility to common antimicrobial agents. Pathogens and potential enteropathogens were identified from 140 (77.8%) of the patients, with more than one pathogen being recovered from 67 (37.2%) patients. Potentially pathogenic parasites were observed in 90 (50%) patients; those that were associated significantly with diarrhoea were Giardia lamblia, Blastocystis hominis, Cryptosporidium spp., Entamoeba histolytica and Cyclospora cayetanensis. Pathogenic bacteria were isolated from 72 (40%) patients, and, of these, 62.5% were resistant to at least one antibiotic, and 30.6% of these were multiresistant. Diarrhoeagenic Escherichia coli strains were found in 14.3% of the patients and 2.9% of the control subjects (not statistically significant). The most common enteropathogenic bacteria found were Shigella spp., Campylobacter jejuni and Yersinia enterocolitica. Unusual bacterial species were the predominant organisms recovered in a few cases and could represent a possible cause of diarrhoea. Overall, there was a high endemicity of diarrhoeal disease in the area studied. Risk factors that correlated significantly with contracting diarrhoea were socio-economic status, education, use of unchlorinated well or tank water, and a low level of personal hygiene.