Although multiple sclerosis (MS) plaques, subacute cerebral ischaemic infarcts, focal vasogenic brain oedema, and subcortical arteriosclerotic encephalopathy (SAE) often have typical radiological patterns, they are sometimes difficult to distinguish from each other. Our aim was to determine whether they can be differentiated by magnetisation transfer (MT) measurements. We measured MT ratios (MTR) in ten patients with plaques of MS, 11 with subacute ischaemic infarcts, 12 with focal vasogenic oedema, and ten with lesions of SAE and compared the mean MTRs statistically. The MTR of normal white matter was 47.3%; the lowest MTR was found in plaques of MS (mean 26.4%). With the exception of vasogenic oedema and subacute cerebral ischaemic infarcts the mean MTRs were significantly different between all groups. MT measurements can provide additional information for the differentiation of these conditions, but we could not distinguish vasogenic oedema from subacute cerebral ischaemic infarcts.