BackgroundMultiple sclerosis is a chronic demyelinating disease that affects the white and grey matter. The thalamus is responsible for many neurological functions, and it is liable to damage in multiple sclerosis in the absence of MRI-detectable thalamic lesions. Standardized imaging protocol for multiple sclerosis includes 3D FLAIR sequence that is highly sensitive in detecting white matter lesions. Owing to the thalamic functional importance, we aim in this study to show to what extent the standardized imaging protocol (3D FLAIR) can predict microscopic damage of normal appearing thalami, depending on DTI metrics (ADC and FA) as indicators of the microscopic damage.ResultsWe examined 42 multiple sclerosis patients, 16 males and 26 females, with mean age 29 ± 6 years using 3D FLAIR sequence to delineate the white matter lesions and calculate their total areas and using DTI to calculate the average ADC and FA values of the thalami. Spearman’s correlation coefficient (r) was used to correlate between the white matter lesion burden and the thalamic diffusivity (ADC and FA).Moderate correlation was found between average ADC values of the thalami and the total white matter lesion areas (r = 0.5, p = 0.03).Very weak correlation was found between average FA values of the thalami and the total white matter lesion areas (r = − 0.1, p = 0.6)ConclusionWhite matter lesion burden detected using the highly sensitive 3D FLAIR sequence does not always correlate with the microstructural damage in normal appearing thalami. DTI needs to be added to the examination protocol if damage of normal appearing thalami is of concern.