BACKGROUND: Environmental enteropathy (EE) is an asymptomatic lesion of the small intestine, likely an adaptive response to environmental noxa, including enteropathogens, leading to recurrent intestinal injury, mucosal inflammation, and microbial translocation. Inflammatory bowel disease (IBD) is increasing in incidence in newly industrialised countries. Given that EE is seen in individuals living in insanitary environments in low-income countries (LICs) and IBD has traditionally been viewed as a disease of developed countries, we hypothesised that these two conditions would not co-exist. AIMS: To investigate whether EE is seen in individuals with IBD living in a low-income country in sub-Saharan Africa. METHODS: Enteropathy was assessed in adult Zambians with IBD and controls from high and low socio-economic status (SES) groups with duodenal biopsies and biomarkers of intestinal and systemic inflammation. Enteropathogen carriage rates between the groups were compared. RESULTS: 28 cases and 59 controls (38 high SES and 21 low SES) were included. Histological features of EE were present in all cases and controls, with median villus height to crypt depth ratio <2 in all groups. Enteropathogen carriage was lower in cases (median of 1 pathogen per case to 2 per control). CONCLUSION: The co-existence of IBD and EE within the same individuals may prove to be a confounding factor when assessing patients presenting with symptoms suggestive of IBD in this setting and could be interpreted as evidence that improved environmental hygiene does not play a significant role in the emergence of IBD.