To assess factors affecting electrophysiological changes in the peripheral nervous system below the neurologic level of injury (NLI) in patients with subacute spinal cord injury (SCI). Retrospective observational study. An inpatient rehabilitation center of a university hospital. Through reviewing the medical records of 151 subjects with SCI, 42 without any other disease inducing peripheral neurologic abnormalities were included. They were classified into 2 groups, with or without denervation potentials in electromyography (EMG) below NLI. Not applicable. Demographics and clinical characteristics including NLI, American Spinal Injury Association Impairment Scale (AIS), and Lower Extremity Motor Score were compared. Results of electrophysiological study including nerve conduction study, somatosensory-evoked potential (SSEP), and motor-evoked potential (MEP) were compared. Denervation potentials in EMG below NLI were observed in 20 subjects, and 10 of them were AIS A or B, but there was none in subjects without denervation potentials (P<.001). The lower extremity motor score was 4.35±7.74 in the group with denervation potentials, lower than 33.64±13.60 of the opposite group (P<.001). In the analysis of electrophysiological study, patients with denervation potentials showed a higher proportion of no response than patients without denervation potentials (60.0% vs 11.4% in peroneal nerve conduction study, 35.0% vs 2.3% in tibial nerve conduction study, 80.0% vs 18.2% in SSEP, 87.5% vs 22.7% in MEP; P<.001, respectively). Additionally, greater axonal loss, based on decrease of amplitude without delayed latency on nerve conduction study, was observed in the group with denervation potentials than the opposite group (P<.001). Among subjects with subacute SCI, cases of peripheral nervous dysfunction below the injury site occur, possibly associated with the severity of SCI.