Aims: The thalamus is a major relay station that modulates input from many cortical areas and a filter for sensory input and is involved in the pathophysiology of amyotrophic lateral sclerosis (ALS). However, it still remains unclear whether all thalamocortical networks are affected or whether there is selective vulnerability. In this study, we aimed to study the selective vulnerability of different thalamocortical structural connections in ALS and to test the hypothesis of a specific impairment in motor-related thalamocortical connectivity. Methods: Diffusion tensor imaging (DTI) tractography was used to identify thalamocortical structural pathways in 38 individuals with ALS and 35 gender/age-matched control subjects. Thalami of both groups were parcellated into subregions based on local patterns of thalamocortical connectivity. DTI measures of these distinct thalamocortical connections were derived and compared between groups. Results: The analysis of probabilistic tractography showed that the structural connectivity between bilateral pre/primary motor cortices and associated thalamic subregions was specifically impaired in patients with ALS, while the other thalamocortical connections remained relatively intact. In addition, fractional anisotropy values of the impaired thalamocortical motor pathway were inversely correlated with the disease duration. Conclusion: Our findings provide direct evidence for selective impairment of the thalamocortical structural connectivity in ALS.