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We performed a longitudinal case-control study on patients with clinically isolated syndrome (CIS) with the aid of quantitative whole-brain myelin imaging. The aim was (1) to parse early myelin decay and to break down its distribution pattern, and (2) to identify an imaging biomarker of the conversion into clinically definite Multiple Sclerosis (MS) based on in vivo measurable changes of myelination. Imaging and clinical data were collected immediately after the onset of first neurological symptoms and follow-up explorations were performed after 3, 6, and, 12 months. The multi-component Driven Equilibrium Single Pulse Observation of T1/T2 (mcDESPOT) was applied to obtain the volume fraction of myelin water (MWF) in different white matter (WM) regions at every time-point. This measure was subjected to further voxel-based analysis with the aid of a comparison of the normal distribution of myelination measures with an age and sex matched healthy control group. Both global and focal relative myelination content measures were retrieved. We found that (1) CIS patients at the first clinical episode suggestive of MS can be discriminated from healthy control WM conditions (p, Highlights • The multicomponent relaxation method mcDESPOT allowed 3D resolved data acquisition appropriate for group comparison and voxel-wise analysis. • Myelin imaging in early clinically isolated syndrome revealed initial imaging widespread myelin loss even in normal appearing brain tissue. • In clinically isolated syndrome the myelin measures varied depending on the presence of Gadolinium enhancement. • Short-term risk of clinically isolated syndrome to convert to multiple sclerosis was determined by myelin measures within white matter lesions.