To facilitate high level analysis of medical image data in research and clinical environments, a wrapper for the ITK toolkit is developed to allow ITK algorithms to be called in MATLAB. ITK is a powerful open-source toolkit implementing state-of-the-art algorithms in medical image processing and analysis. However, although ITK is rapidly gaining popularity, its user base is mostly restricted to technically savvy developers with expert knowledge of C++ and advanced programming concepts. MATLAB, on the other hand, is well-known for its easy-to-use, powerful prototyping capabilities that significantly improve productivity. Unfortunately, the 3D image processing capabilities of MATLAB are very limited and slow to execute. With the help of the wrapper we introduce in this paper, biomedical computing researchers familiar with MATLAB can harness the power of ITK while avoiding learning C++ and dealing with low-level programming issues. We strongly believe this functionality will be of considerable interest to the medical image computing community. In this paper we provide details about the design and usage of this interface in medical image filtering, segmentation, and registration.