Background: In patients with a C9orf72 repeat expansion (C9+), a neuroimaging phenotype with widespread structural cerebral changes has been found. We aimed to investigate the specificity of this neuroimaging phenotype in patients with amyotrophic lateral sclerosis (ALS). Methods: 156 C9- and 14 C9+ patients with ALS underwent high-resolution T1-weighted MRI; a subset (n=126) underwent diffusion-weighted imaging. Cortical thickness, subcortical volumes and white matter integrity were compared between C9+ and C9-patients. Using elastic net logistic regression, a model defining the neuroimaging phenotype of C9+ was determined and applied to C9-patients with ALS. Results: C9+ patients showed cortical thinning outside the precentral gyrus, extending to the bilateral pars opercularis, fusiform, lingual, isthmus-cingulate and superior parietal cortex, and smaller volumes of the right hippocampus and bilateral thalamus, and reduced white matter integrity of the inferior and superior longitudinal fasciculus compared with C9-patients (p<0.05). Among 128 C9-patients, we detected a subgroup of 27 (21%) with a neuroimaging phenotype congruent to C9+ patients, while 101 (79%) C9-patients showed cortical thinning restricted to the primary motor cortex. C9-patients with a 'C9+' neuroimaging phenotype had lower performance on the frontal assessment battery, compared with other C9-patients with ALS (p=0.004). Conclusions: This study shows that widespread structural brain involvement is not limited to C9+ patients, but also presents in a subgroup of C9-patients with ALS and relates to cognitive deficits. Our neuroimaging findings reveal an intermediate phenotype that may provide insight into the complex relationship between genetic factors and clinical characteristics.