A major driver of the link between poor water, sanitation and hygiene (WASH) and child stunting is hypothesised to be a sub-clinical condition of the small intestine termed environmental enteric dysfunction (EED). This systematic review aimed to collate research investigating the association between biomarkers of EED and child linear growth outcomes. A systematic search of literature was conducted to identify articles that contain a measure of a domain of EED and its association with linear growth outcomes published up to 31 December 2024. Data pertaining to the measure of EED and child linear growth, as well as study characteristics, were extracted and tabulated. A total of eighty-one studies comprising 31 996 children were included, which suggested that all EED domains, including intestinal damage and repair, intestinal absorption and permeability, microbial translocation, intestinal inflammation and systemic inflammation, were associated with child linear growth. Nuances in the measurement of association were apparent and impacted the observation of significant associations. This review found that whilst the role of EED in child stunting is relatively well established, there are challenges faced in measuring biomarkers in relation to linear growth with possible ambiguities. These issues are discussed in detail to provide aid in interpretation of existing studies and to inform future studies of this kind.