Spinal cord injury (SCI) has profound effects upon cardiovascular autonomic function due to injury to descending autonomic pathways, and cardiovascular diseases are the leading causes of morbidity and mortality after SCI. The evaluation of cardiovascular autonomic dysfunction after SCI, and the appraisal of simple non-invasive autonomic assessments, that are clinically meaningful, would be useful to SCI clinicians and researchers. We aimed to assess supine and upright cardiovascular autonomic function from frequency analyses of heart rate (HRV) and blood pressure (BPV) variability after SCI. We studied 26 subjects with chronic cervical or thoracic SCI, and 17 able-bodied controls. We continuously recorded RR interval (RRI; electrocardiogram) and beat-to-beat blood pressure (Finometer) while supine and seated. Cardiovascular control was assessed from spectral analysis of RRI and blood pressure time series. Cardiac baroreflex control was assessed from cross-spectral analyses of low frequency spectra. Supine and upright low frequency HRV and BPV were reduced in cervical SCI, as were total BPV and HRV. Supine high frequency HRV was reduced in thoracic SCI. Cardiac baroreflex delay was increased in cervical SCI. Supine frequency domain indices were correlated with sympathetic skin responses, orthostatic cardiovascular responses, and plasma catecholamine levels. SCI results in reduced sympathetic drive to the heart and vasculature and increased baroreflex delay in cervical SCI, and reduced cardiac vagal tone in thoracic SCI. Frequency analyses of autonomic function are related to clinical measures of autonomic control after SCI, and provide useful non-invasive clinical tools with which to assess autonomic completeness of injury following SCI.