The structures of buckwheat and barley were observed by Scanning Electron Microscopy (SEM) and Confocal Scanning Laser Microscopy (CSLM) throughout the malting process. SEM and CSLM have different merits when studying grains and seeds. SEM can be used to study the detailed structure (high magnifications can be achieved) and CSLM to study the overall change in structure during processing. SEM proved that buckwheat starch is degraded by both pitting and surface erosion. A concentric sphere structure was visible when buckwheat starch granules were partly broken down. With CSLM, the organization of protein and starch of buckwheat and barley could be examined independently in projections and images visualizing the 3D structure. CSLM proved that buckwheat starch is surrounded by a protein matrix. Buckwheat protein was structured and surrounded starch granules, while barley protein was present in an amorphous mass through the endosperm. The differences in overall structure between unmalted and malted seeds were evident, as the starch and protein in both the barley and buckwheat were degraded. CSLM may be used in the future to couple processing characteristics to the structure of grains and seeds..