The purpose of this study was to examine the impact of emulsifier type on the micro-structural changes that occur to emulsified lipids as they pass through a model gastrointestinal system. Lipid droplets initially coated by different kinds of emulsifiers (lecithin, Tween 20, whey protein isolate and sodium caseinate) were prepared using a high speed blender. The emulsified lipids were then passed through an in vitro digestion model that simulated the composition (pH, minerals, surface active components, and enzymes) of mouth, stomach and small intestine juices. The change in structure and properties of the lipid droplets were monitored by laser scanning confocal fluorescence microscopy, conventional optical microscopy, light scattering, and micro-electrophoresis. In general, there was a decrease in mean droplet diameter (d32) as the droplets moved from mouth to stomach to small intestine. The electrical charge on the droplets stabilized by lecithin, Tween 20 and sodium caseinate were negative throughout the model GI system, while those stabilized by whey protein were positive in the stomach. This suggests that at least some of this globular protein remained attached to the droplet surfaces. The data was interpreted in terms of the competitive adsorption of phospholipids/bile salts with the adsorbed emulsifiers, as well as the enzymatic digestion of proteins and lipids. These results enhance our understanding of the physicochemical and structural changes that may occur to emulsified lipids within the gastrointestinal tract, which may have important consequences for the design of functional foods that alter lipid bioavailability. Nevertheless, there were appreciable differences between the behavior of emulsions within the in vitro model used in this study and literature reports of their behavior within in vivo studies, which highlights the need for more realistic in vitro digestion models.