Structural changes in insoluble cell walls, and rheological changes occurring during incubation of unyeasted wholemeal rye doughs were studied by fluorescence microscopy, image analysis and dynamic visco-elastic measurements. Three samples were chosen to represent a range of sprouting resistance and type of rye. Ensi is an old Finnish rye variety, with poor resistance to sprouting, Anna is typical of current Finnish breadmaking varieties, whilst Amando represents a new German hybrid variety, with good resistance to sprouting. Microstructural studies of grain cross sections indicated that even before milling, great structural damage had occurred in the cell walls of Ensi, the sample with the lowest falling number (62). The blue fluorescence, present in intact cell walls, was absent in the subaleurone layer and in the cells of ventral endosperm. In the dough of Amando, the sample with the highest falling number (299), the area of fluorescing cell walls was greatest and it was lowest in that of Ensi with the lowest falling number; Anna (falling number 187) resembled Amando more than Ensi. The storage modulus (G′) decreased with increasing water content for all samples, with the phase angle showing a corresponding increase. During incubation the area of cell walls decreased and the doughs became softer, as indicated by visco-elastic measurements. Changes in G′ during incubation were largest in the Ensi dough at all studied water contents, whereas Amando and Anna showed approximately the same change.