Abstract Conventional MRI is crucial for diagnosing multiple sclerosis (MS) but lacks precision, leading to the clinico-radiological paradox and misdiagnosis risk, especially when confronted with unspecific lesions not related to MS. Advancements in perfusion-weighted imaging (PWI) with an algorithm designed for diseases with anticipated contrast agent extravasation offer insight into microvascular impairment and flow heterogeneity. Our study aimed to assess these factors in MS patients and their association with clinically relevant white matter injury and disease course. We evaluated 60 adults with white matter lesions (WML), including 50 diagnosed with MS or MS syndromes and 10 non-diseased symptomatic controls (SC) with unspecific WML. MRI included conventional three-dimensional (3D) T2-weighted fluid-attenuated inversion recovery (T2-FLAIR), 3D magnetization-prepared 2 rapid acquisition gradient-echo (MP2RAGE), post-contrast 3D T1-weighted (T1) images and Dynamic Susceptibility Contrast (DSC) PWI at 3T. WML masks of “unspecific T2-FLAIR lesions”, “MS T2-FLAIR lesions”, and “MS T1-lesions” were manually outlined and validated by a neuroradiologist. DSC-derived parameters were analyzed in WML masks and healthy-appearing tissue. MS T2-FLAIR lesions showed increased flow heterogeneity and vasodilation compared to unspecific T2-FLAIR lesions in SC, as well as compared to unspecific T2-FLAIR lesions within the MS group. MS T1-lesions exhibited more homogenized flow. Our findings suggest that DSC-PWI combined with lesion delineation, can provide clinically relevant differentiation of MS lesions from unspecific WML, highlighting potential microvascular pathology previously overlooked in MS.