The location and penetration patterns of two fluorescently-labelled, surface active molecules into normal and waxy wheat starch granules prior, during and after the temperature-induced gelatinisation were studied by means of confocal laser scanning microscopy (CLSM). Amphiphilic dyes were found to have a tendency to penetrate wheat starch granules in aqueous suspension. The penetration patterns were however found to be dependent on the contact time, type of starch and the chain length of the amphiphilic dye. The penetration of amphiphilic dyes through the starch granule matrix proved to be less restricted in waxy than in normal wheat starch. For a given type of starch, the penetration of the longer chain dye was more constrained than that of the shorter chain one. The extent to which the dye diffuses into the granule matrix as it gelatinizes is also affected by the chain length of the dye, diffusion of the shorter chain dye occurring more profusely and at lower temperatures than for the longer chain one. These differences are suggested to be related to the dissociation temperature of the AM-amphiphilic dye complexes.