We identified a distinct pattern of enteropathy biomarkers in HEU compared to HIV-unexposed infants, characterised by more intestinal inflammation (raised faecal neopterin; Tobit β 1.39; 95% CI 1.14, 1.69, P = 0.001), differences in small intestinal villous damage (lower stool I-FABP; Tobit β 0.79; 95% CI 0.72, 0.87, P < 0.001) and some evidence of heightened epithelial regeneration (raised faecal REG-1β; Tobit β 1.47; 95% CI 0.95, 2.28, P = 0.088). This evidence concerns the gene FABP2 and Abnormal intestine morphology.