Conventional MR imaging techniques still lack specificity for the underlying central nervous system tissue damage in multiple sclerosis (MS), impeding a comprehensive investigation of the key mechanisms responsible for neurological disability such as myelin damage and repair, neurodegeneration and neuroinflammation. A range of novel and advanced imaging tools, using quantitative magnetic resonance (MR) or positron emission tomography (PET) technologies are now emerging and open the perspective to obtain unique insights into the disease mechanisms. Both can be employed either in experimental models or in patients with MS, and they have already allowed to obtain imaging metrics that significantly correlate with clinical scores. In this review, we summarize the main evidence supporting the use of quantitative MR and PET as essential investigation tools to explore myelin changes, neuronal damage and compartmentalized inflammation in MS. The clinical translation of these imaging techniques has the potential to improve the design of future clinical trials and to allow the measurement of the effects of new drugs aimed at enhancing myelin repair and reducing neurodegeneration and neuroinflammation.