Multiple Sclerosis (MS) pathology is complex and includes inflammatory processes, neurodegeneration, and demyelination. While multiple drugs have been developed to tackle MS-related inflammation, to date there is scant evidence regarding which therapeutic approach, if any, could be used to reverse demyelination, foster tissue repair, and thus positively impact on chronic disability. Here, we reviewed the current structural and functional markers (magnetic resonance imaging, positron emission tomography, optical coherence tomography, and visual evoked potentials) which could be used in phase II clinical trials of new compounds aimed to foster tissue repair in MS. Magnetic transfer ratio recovery in newly formed lesions currently represents the most widely used biomarker of tissue repair in MS, even if other markers, such as optical coherence tomography and positron emission tomography hold great promise to complement magnetic transfer ratio in tissue repair clinical trials. Future studies are needed to better characterize the different possible biomarkers to study tissue repair in MS, especially regarding their pathological specificity, sensitivity to change, and their relationship with disease activity.