PURPOSE: To define differences in heart rate and blood pressure variability (HRV/BPV) after spinal cord injury (SCI) compared with uninjured controls, and to determine whether variabilities are impacted by whole-body exercise after SCI. METHODS: Individuals with SCI (n = 40), aged 18-40, and uninjured age/sex-matched controls (n = 22) had HRV and BPV determined during supine paced (0.25 Hz) breathing. Spectral and cross-spectral values were derived for fluctuations at low (LF 0.05-0.15 Hz) and high (HF 0.20-0.30 Hz) frequencies. Thirty-two individuals with SCI further underwent either 6 months of whole-body exercise training (n = 17) or a control intervention (n = 15). RESULTS: Individuals with SCI had injuries graded A-C in severity, neurological levels of injury C1-T10. LF and HF HRV and LF BPV were significantly lower in individuals with SCI (p = 0.008-0.002), though HF BPV was similar. The LF cross-spectrum demonstrated similar phase and gain relationships between groups. The HF phase relationship between pressure and heart rate differed markedly: individuals with SCI demonstrated a -11.7 +/- 3.4 degrees phase lag (241 +/- 70 ms feedback mechanism of pressure into heart rate), whereas uninjured controls demonstrated a +21.5 +/- 10.8 degrees phase lead (443 +/- 224 ms feedforward mechanism of heart rate into pressure, p = 0.007). Whole-body exercise increased mean VO(2peak) by 2.09 ml/kg, whereas HRV, BPV, and their cross-spectral relationships were not significantly altered relative to the control intervention after SCI. CONCLUSION: After SCI, marked frequency-specific differences exist in the relationship between heart rate and blood pressure variabilities. The high-frequency cross-spectral relationship indicates that a feedback mechanism of blood pressure into heart rate may predominate in this range.