The coupling between structure and diffusion properties is essential for the functionality of heterogeneous biomaterials. Structural heterogeneity is defined and its implications for time-dependent diffusion are discussed in detail. The effect of structural heterogeneity in biomaterials on diffusion and the relevance of length scales are exemplified with regard to different biomaterials such as gels, emulsions, phase separated biopolymer mixtures and chocolate. Different diffusion measurement techniques for determination of diffusion properties at different length and time scales are presented. The interplay between local and global diffusion is discussed. New measurement techniques have emerged that enable simultaneous determination of both structure and local diffusion properties. Special emphasis is given to fluorescence recovery after photobleaching (FRAP). The possibilities of FRAP at a conceptual level is presented. The method of FRAP is briefly reviewed and its use in heterogeneous biomaterials, at barriers and during dynamic changes of the structure is discussed.