Virtual endoscopy (VE) enables non-invasive 3D endoluminal imaging of the middle ear by post-processing of CT data. To optimise the clinical application a standardised approach was evaluated in normal and pathologic cases. Data acquisition was performed using multi-slice helical CT in 20 normal patients and 15 patients with malformation or trauma. Virtual endoscopy of the tympanic cavity and 3D images of the ossicles were generated using surface and volume rendering. Qualitative assessment of the representation of anatomical structures was performed in normal patients. In 15 pathological cases the diagnostic benefit was evaluated by comparing the 3D images to the 2D images and intra-operative findings. In all 35 cases 3D imaging was possible using the standardised approach. The ossicular chain as well as the bony and soft tissue structures of the tympanic cavity were visualised in 20 normal patients. In 7 of 8 patients with malformation and 1 of 7 patients with trauma the original diagnosis was changed by 3D imaging. Standardisation and evaluation of the method in normal patients is essential as it enhances the diagnostic reliability. Virtual endoscopy facilitates understanding of the complex anatomy of the middle ear. In cases of suspected malformation and confirmed trauma it is helpful for diagnosis and surgical planning.