Scope The epithelial glycocalyx development is of great importance for microbial colonization. Human milk oligosaccharides (hMOs) and non-digestible carbohydrates (NDCs) may modulate glycocalyx development. Methods and results The effects of hMOs and NDCs on human gut epithelial cells (Caco2) are investigated by quantifying thickness and area coverage of adsorbed albumin, heparan sulfate (HS), and hyaluronic acid (HA) in the glycocalyx. Effects of hMOs (2 '-FL and 3-FL) and NDCs [inulins with degrees of polymerization (DP) (DP3-DP10, DP10-DP60, DP30-DP60) and pectins with degrees of methylation (DM) (DM7, DM55, DM69)] are tested using immunofluorescence staining at 1 and 5 days stimulation. HMOs show a significant enhancing effect on glycocalyx development but effects are structure-dependent. 3-FL induces a stronger albumin adsorption and increases HS and HA stronger than 2 '-FL. The DP3-DP10, DP30-60 inulins also increase glycocalyx development in a structure-dependent manner as DP3-DP10 selectively increases HS, while DP30-DP60 specifically increases HA. Pectins have less effects, and only increase albumin adsorption. Conclusion Here, it is shown that 2 '-FL and 3-FL and inulins stimulate glycocalyx development in a structure-dependent fashion. This may contribute to formulation of effective hMO and NDC formulations in infant formulas to support microbial colonization and gut barrier function.