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The aim of the study was to develop novel zeta potential changing self-emulsifying drug delivery systems (SEDDS) containing phosphorylated polysaccharides.Starch and hydroxypropyl starch (HPS) were phosphorylated by utilizing phosphorus pentoxide. The modified starches, starch phosphate (SP) and hydroxypropyl starch phosphate (HPSP), were loaded into SEDDS and investigated regarding particle size, zeta potential, stability and cell viability. The release of immobilized phosphate by intestinal alkaline phosphatase (IAP) was analyzed via malachite green assay. In parallel, the resulting shift in zeta potential of SEDDS was determined. Furthermore, Transwell chambers were applied in order to evaluate the mucus diffusion behavior of SEDDS utilizing fluorescein diacetate (FDA) as marker.The amount of attached phosphate for SP and HPSP revealed to be 119 μmol/g and 259 μmol/g, respectively. SEDDS consisting of 10% glycerol, 30% Capmul MCM, 30% Cremophor EL and 30% Captex 355 showed a droplet size of 39 ± 12 nm, stability over 240 min and no significant decrease in cell viability within the applied concentrations. SEDDS containing 3 mg/ml HPSP with a phosphate release of 204 μmol/g, demonstrated a shift in zeta potential from -6.3 mV to + 1.0 mV applying isolated IAP. Zeta potential changing SEDDS achieved a 2.5-fold and 5.4-fold higher amount of diffused FDA compared to the references within mucus permeation studies.SEDDS containing HPSP represent comparable high mucus diffusion properties emphasized by a highly significant change in zeta potential.