Technologies for imaging in three dimensions are greatly desired by researchers in many biological disciplines. However, when imaging small animals such as invertebrates, the achievement of satisfactory spatial resolution and adequate contrast between tissues often requires the use of expensive and time-consuming procedures. Micro-X-ray-computed tomography (muCT) is a convenient technique which is finding greater use alongside conventional microscopies. Staining with heavy metal salts, such as osmium tetroxide improves imaging in muCT, and allows visualization of the 3D structure of the honey bee brain undistorted within the intact head capsule. We obtained detailed information about the morphology of the different brain compartments and were able to show their orientations, relative to each other, within the head capsule. This technique offers a significant improvement in resolution, time, and expense for the quantitative, three-dimensional analysis of developing bee brain centers. In this article, we introduce a rapid, high-resolution, and inexpensive technique for the three-dimensional visualization of different compartments of the honey bee brain. A detailed discussion of the honey bee brain anatomy is provided, demonstrating that muCT, with osmium staining, can indeed visualise these structures. Hence, our results show that muCT is ideally suited for researchers who are interested in the 3D visualization of small invertebrate brains.