Conditioning of lower limb H-reflexes by transcranial magnetic stimulation of motor cortex was used to detect preserved innervation in patients with long-standing spinal cord injury (SCI). Cortical stimulation was delivered at intensities suprathreshold or subthreshold for evoking motor evoked potentials (MEPs). The conditioning (C) cortical stimulation preceded the test (T) H-reflex stimulus at intervals between C-T: 10-300 msec. Conditioned H-reflex profiles in control subjects (n = 10), following both suprathreshold and subthreshold cortical conditioning, yielded evidence of early (C-T: 10-30 msec) and late arriving (C-T: 60-130 msec) excitatory inputs to the lateral gastrocnemius (LG) motoneuron pool. Demonstration of late inputs following subthreshold cortical conditioning suggested the inputs are mediated by slow conducting or oligosynaptic descending motor tracts, as distinct from afferent consequences of short latency MEPs. In SCI patients (n = 11) the conditioned H-reflex profile varied according to the patients' ASIA impairment rating. Higher functioning SCI patients (ASIA level C and D) revealed evidence of both early and late arriving inputs to the lumbosacral motoneuron pool whereas patients with more severe impairments (ASIA levels A and B) most often failed to exhibit early or late periods of H-reflex facilitation in LG. In three patients (i.e., 1 ASIA B; 2 ASIA C) the cortical modulation of H-reflex amplitudes yielded evidence of preserved corticospinal innervation that was not detectable by other MEP reinforcement procedures. These results introduce the cortical conditioning procedure as a sensitive means of detecting latent corticospinal and/or bulbospinal innervation in SCI patients consistent with the emerging neuropathological picture of preserved axonal integrity in descending motor tracts in the face of extensive functional loss.