Magnetic Resonance Imaging (MRI) has become an important tool in the diagnosis of inflammatory CNS diseases such as Multiple Sclerosis (MS) and HTLV-1 Associated Myelopathy/Tropical Spastic Paraparesis (HAM-TSP). It is widely used as a marker for disease activity and progression. However, conventional MRI methods are only suitable to study gross anatomical features, such as size and shape of a particular area of the brain; questions regarding intrinsic microstructure and morphologic specificity cannot be addressed. But axonal damage or structural abnormalities even in normal appearing brain tissue may play an important role in the development of irreversible disability. Magnetization Transfer Imaging, Magnetic Resonance Spectroscopy and Diffusion Tensor MRI are imaging techniques described to be capable of the detection of such changes. Spectroscopy can detect molecular components in tissue, whereas the Magnetization Transfer Ratio (MTR) allows the measurement of water-macromolecule interactions. Diffusion Tensor MRI (DT-MRI) is an imaging modality that combines features of in vivo anatomical MRI and histopathology: it is an in vivo MRI method that provides information about tissue composition, microstructure, organization and architecture. This is possible because water diffusion properties in tissues, as measured by DT-MRI, are affected by tissue constituents, such as macromolecules, membranes, organelles, as well as by tissue microstructure, architecture and organization. A study comprising Magnetization Transfer-, Spectroscopy- and DT-MRI furnishes important information that cannot be obtained using conventional MRI methods.