The effect of a protein based fat substitute (Simplesse® 100) incorporated at a 1.5% level (w/w) in set-style yogurt on its microstructure, syneresis and firmness was compared with the effect of anhydrous milk fat (AMF) used at the same concentration. The fat substitute was used in both commercial forms available, ie, as a dry or a wet ingredient. The yogurt bases consisted of reconstituted skimmed milk powder including the added ingredients and contained 14.3–15.5% total solids. Electron microscopy revealed that homogenization of AMF produced fat globules which interacted with milk proteins present in the yogurt base and thus the fat became an integral part of the yogurt microstructure. Similar integration was observed with the fat substitute, the particles of which (0.1–3 μm in diameter) were found to be parts of the casein micelle chains or spanned adjacent chains. These chains were found to be somewhat shorter (no statistical assessment was carried out) in the yogurts made with the fat substitute in wet or dry forms than in the yogurt made with AMF. Yogurts with the fat substitute were softer than the yogurts containing AMF, although their composition was similar except for the fat which was replaced with the fat substitute.