Two rye cultivars, Marder and Motto, with falling numbers 314 and 309, respectively, were germinated in vitro. Relative to the native grains, germination induced minor local changes in the microstructure of cell walls and proteins in the kernels. Kernels of germinated and native grains were milled, and doughs were prepared from the flours, with water content and incubation time varied according to experimental design. The viscoelastic properties of the doughs were measured just after mixing and after various incubation times. The area of blue fluorescence, a measure of intact cell walls, was quantified by computer‐assisted image analysis in thin sections of rye dough after mixing and incubation, and the starch structure was studied under the microscope after iodine staining. The water content of the doughs was explained well by the rheological behavior. Doughs made from flours of germinated grains were always softer than doughs made from flours of native grains, and Marder doughs were always more rigid than Motto doughs. The higher the water content, and the longer the incubation time, the greater the rheological changes during incubation. Microstructural studies showed that germination and incubation caused changes in the cell wall structures of dough that might explain the softening of the doughs.