A research area of increasing interest consists of studying the benefits of using spectral analysis to screen neurogenic erectile dysfunctions. Our hypothesis is that spectral analysis consists of a non-invasive and simple procedure to investigate such patients. Subjects were allocated into two groups: control, no erectile dysfunction (n = 17), and patients with erectile dysfunction (n = 15). RR intervals (RRI), systolic blood pressure, diastolic blood pressure and baroreflex sensitivity recordings were performed continuously in the supine position, followed by the seated position, and finally standing position. In the supine position, the control group had a higher RRI and a lower diastolic blood pressure. For frequency domain analyses of RRI in the supine position, the erectile dysfunction group had a higher normalized low-frequency (LF) index and low-frequency/high-frequency (LF/HF) ratio while showing a lower normalized HF index. In the seated position, the erectile dysfunction group presented a higher LF/HF ratio. Regarding systolic blood pressure, the erectile dysfunction group showed lower normalized LF and higher normalized HF indices only in the supine position. The α index in HF was lower in the erectile dysfunction group in the three positions. Spectral analyses of cardiac sympathovagal drive constitute a fruitful non-invasive approach to evaluate alterations in cardiovascular autonomic modulation in neurogenic erectile dysfunction patients.