Introduction: To test the hypothesis of impaired cholinergic activity in amyotrophic lateral sclerosis (ALS), we studied short‐ and long‐latency afferent inhibition (SAI and LAI). Methods: The ulnar nerve was stimulated at the wrist preceding transcranial magnetic stimulation (TMS), 21 ms for SAI and 200 ms for LAI, in 21 patients and 17 control subjects. Short‐interval intracortical inhibition (SICI) and cognitive function was assessed in ALS patients using automatic threshold tracking and the Montreal Cognitive Assessment (MoCA). Results: The SAI paradigm resulted in inhibition in all control subjects, whereas inhibition was observed in 13 of 21 (62%) patients. Mean SAI and LAI values were significantly reduced in ALS. No significant correlation existed between afferent inhibition and other neurophysiological data. The MoCA was normal in all but 1 patient. Discussion: LAI and SAI are both impaired in ALS, probably unrelated to increased cortical excitability or cognitive dysfunction. Muscle Nerve 59:699–704, 2019