Background Gut bacteria Bifidobacterium longum, Faecalibacterium prausnitzii, Dorea formicigenerans and Akkermansia muciniphila have been implicated in mediation of growth. We investigate the prevalence of these four species, levels of fecal biomarkers of environmental enteric dysfunction (EED) and association with stunting in rural Malawian children. Methods DNA and protein were extracted from fecal samples of 613 children (aged 1-59 months) at a baseline cross-sectional survey in the Mangochi district of Malawi conducted within the framework of the MORDOR (Macrolides Oraux pour Réduire les Décès avec un Oeil sur la Résistance) trial. Intestinal carriage of bacteria was measured by PCR. Neopterin, myeloperoxidase and alpha-1 antitrypsin, biomarkers of EED, were measured by ELISA. Height-for-age Z (HAZ) score <-2 defined stunting. Tests of proportions and regression models were used to explore the relationship between bacterial carriage, EED and stunting. Results B. longum carriage in younger children was associated with elevated EED biomarkers. Two thirds of children had elevated NEO, 33% elevated MPO and 16% elevated AAT. Stunting was found in 38% of the children. No significant associations were found between EED biomarkers or intestinal bacteria carriage and stunting.