Background. Available data from murine studies suggest that intestinal bacteria may have a role in modulating growth phenotypes in the host. We investigated the prevalence of four gut bacteria known in murine models to impair growth (Bifidobacterium longum, Faecalibacterium prausnitzii, Dorea formicigenerans, and Akkermansia muciniphila), the level of fecal biomarkers of environmental enteric dysfunction (EED) and stunting in rural Malawian children. Methods. DNA and protein were extracted from fecal samples of rural Malawian children (aged 1-59 months) at a baseline cross-sectional survey in the Mangochi district of Malawi conducted within the framework of the Macrolides Oraux pour Réduire les Décès avec un Oeil sur la Résistance (MORDOR) trial. Intestinal carriage of bacteria was measured by PCR. Neopterin (NEO), myeloperoxidase (MPO), and alpha-1 antitrypsin (AAT), biomarkers of EED, were measured by an enzyme-linked immunosorbent assay (ELISA) test. 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. Fecal samples from 613 children were available for laboratory analyses. F. prausnitzii and D. formicigenerans were prevalent in over 70% of children while B. longum was the least prevalent. B. longum carriage in younger children was associated with elevated EED biomarkers. Two thirds of children had elevated NEO, 33% had elevated MPO, and 16% had elevated AAT. Stunting was found in 38%. No significant associations were found between EED biomarkers or intestinal bacteria carriage and stunting. Conclusion. Intestinal carriage of these four bacteria was not associated with stunting in Malawian children. Carriage was also not associated with EED, nor EED biomarker levels associated with stunting. Further factors acting in concert are necessary to impact EED, perturb growth, and alter gut bacterial carriage.