Yogurt was made using an exopolysaccharide-producing strain of Streptococcus thermophilus and its genetic variant that only differed from the mother strain in its inability to produce exopolysaccharides. The microstructure was investigated using confocal scanning laser microscopy, allowing observation of fully hydrated yogurt and the distribution of exopolysaccharide within the protein network. Yogurt made with the exopolysaccharide-producing culture exhibited increased consistency coefficients, but lower flow behavior index, yield stress, viscoelastic moduli and phase angle values than did yogurt made with the culture unable to produce exopolysaccharide. The exopolysaccharides, when present, were found in pores in the gel network separate from the aggregated protein. These effects could be explained by the incompatibility of the exopolysaccharides with the protein aggregates in the milk. Stirring affected the yogurt made with exopolysaccharide differently from yogurt without exopolysaccharide, as it did not exhibit immediate syneresis, although the structural breakdown was increased. The shear-induced microstructure in a yogurt made with exopolysaccharide-producing culture was shown to consist of compartmentalized protein aggregates between channels containing exopolysaccharide, hindering syneresis as well as the buildup of structure after stirring.