Imaging of the delicate inner ear morphology has become more and more precise owing to the rapid progress in magnetic resonance imaging (MRI). However, in clinical practice, the interpretation of imaging findings is hampered by a limited knowledge of anatomical details which are frequently obscured by artifacts. Corresponding review articles are as rare in journals as they are in reference books. This shortness prompted us to perform a direct comparison of imaging with anatomical whole-mount sections as a reference. It was the intention of this paper to compare the microscopic anatomy of a human inner ear as shown on anatomical whole-mount sections with high-resolution MRI and cone beam computed tomography (CBCT). Both are available in clinical routine and depict the structures with maximum spatial resolution. It was also a goal of this work to clarify if structures that were observed on MRI in a regular manner correlate with factual inner ear anatomy or correspond with artifacts typical for imaging. A fresh human anatomical specimen was examined on a clinical 3-Tesla MRI scanner using a dedicated surface coil. The same specimen was then studied with CBCT. In each imaging modality, high-resolution 3D data sets which enabled multiplanar reformatting were created. In the second step, anatomical whole-mount sections of the specimen were cut and stained. This process enabled a direct comparison of imaging with anatomical conditions. Clinical MRI was able to depict the inner ear with remarkable anatomical precision. Strongly T2-weighted imaging protocols are exquisitely capable of showing the fluid-filled components of the inner ear. The macular organs, ampullar crests and cochlear aqueduct were clearly visible. Truncation artifacts are prone to be confused with the delicate membrane separating the endolymphatic from the perilymphatic compartment. However, it was not possible to directly depict this borderline. With the maximum resolution of magnetic resonance tomography, commonly used in everyday clinical practice, even the smallest details of the inner ear structures can be reliably displayed. However, it is important to distinguish between truncation artifacts and true anatomical structures. Therefore, this study can be useful as a reference for image analysis.