We aimed in this study to assess the clinical usefulness of fractional anisotropy (FA) maps in the evaluation of lacunar infarctions in striatum, internal capsule and thalamus. We retrospectively reviewed 28 patients (18 men, 10 women; mean age 63 years) who had acute lacunar infarction in striatum, internal capsule and thalamus on diffusion weighted MR imaging (DWI). Fractional anisotropy (FA) maps were generated in addition to conventional T2 weighted images (T2WI) and trace maps of DWI. Two radiologists reviewed the location of infarcts in combination with and without FA maps. Exact location of infarction was determined by FA maps, i.e. on the white band of internal capsule or outside the internal capsule. Accuracy and inter-observer agreement on determination of the location of infarction was evaluated. Accuracy of infarct localization by T2WI-DWI only was varied from 72 to 91% according to the observers. Inter-observer agreement value was moderate (Kappa=0.446), when images were interpreted by T2WI-DWI only. Clinical manifestation of each lesions were varied, but sensory motor stroke was mainly observed in thalamic lesion (50%), while pure motor hemiparesis was predominant in the case of infarct involving internal capsule, corona radiata (91%) and basal ganglia (83%). The FA map is useful in the evaluation of lacunar lesions in striatum, internal capsule and thalamus. Clinical presentation varies according to the exact location of lacunar infarctions, and more accurate diagnosis can be made by FA maps as well as conventional T2-weighted image and DWI.