The amount of measurement data collected in medical diagnostics makes their storage and handling an important issue. Also, the requirements for the visualization of such data, and for merging information from different sources of measurement, are growing. In the case of diagnosis of stomatognathic system we have to deal with various methods of medical imaging, such as CT, 3D scans, impressions of teeth, facial scans, and various types of reconstructions resulting from processing of measurement data. In the research project dedicated to the diagnosis of bruxism, we encounter records of measurements of Holter monitoring. We present a web application designed to collect the measurement data acquired in the project. In the first version, this tool has been prepared to store EKG files. We are planning further extension of the capabilities of the database to collect 3D scans, volumetric data and surfaces which are reconstructed from computed tomography. We also present assumptions for the user interface to the desktop application to assist the diagnosis. The application will allow to carry out morphometric measurements, the integration of multimodal imaging data, visualization of mandible movement in TMJ, occlusion detection and motion simulation of the mandible, and also the design of dental guard.