Two juvenile baboons presented with diarrhoea, which did not resolve completely following antibiotic therapy. Ileal intussusception was identified at autopsy in both cases. Trichuris was the only gastrointestinal pathogen for which evidence could be found. This helminth is well-recognized as a cause of intussusception in human infants, but the complication has not been reported previously in non-human primates. It is likely to be fatal if undiagnosed.