NMR microscopy provides non-invasively distinct soft-tissue contrast in small biological samples. We were able to visualize the three-dimensional structure of the honeybee brain in its natural shape in the intact head capsule. Thus, in addition to acquiring detailed information about the shapes and volumes of the different brain compartments, we were able to show their relative orientations toward each other within the head capsule. Since the brain was lightly fixed but not dehydrated, and stayed attached to the head capsule and its internal structures, the NMR experiments exhibited larger volumes and a more natural stereo geometry of the various brain structures compared to confocal laser microscopy experiments on dissected, dehydrated and cleared brains.