The diffusion of solutes through milk and milk-derived media (i.e. dairy systems) is an important factor in the transformation and stabilization of dairy products. In several polymer systems, the diffusion of solutes largely depends on the microstructure within the material. The aim of this work was to establish how the diffusion of solutes is affected by the microstructure of dairy systems. Diffusion measurements were carried out using the technique of fluorescence recovery after photobleaching (FRAP). Diffusion coefficients of a range of 8 fluorescein isothiocyanate (FITC)–dextrans (molecular weights from 4 to 2000 kDa) were measured in dairy systems. These systems had the same casein concentration (130 g kg−1) and water activity but their microstructure had been altered by different treatments: heat-treatment and rennet-induced coagulation. Microstructural parameters of these systems were estimated by the image analysis of transmission electron microscopy (TEM) micrographs. The results showed that the diffusion of solutes was affected by the microstructure of dairy systems. The application of heat-treatment hindered the diffusion of all solutes (irrespective of molecular weight), whereas rennet coagulation only increased the diffusion of the larger solute molecules (N20 kDa). At the microscopic scale, the diffusion of solutes in dairy systems was mainly explained by both the pore size within the structure and by the interface area between the solutemolecules and the surroundingmatrix. Larger solutes diffused faster in dairy systems with larger pore sizes and less interface area.