The RT interval is a measure of the ventricular repolarization and is partially influenced by the sympathovagal balance. The analysis of the variation of the duration of the RT and RR intervals might bring new information about the arrhythmogenic vulnerability and autonomic imbalance. The RR signal and its spectral density (SD) are characterized by two different patterns during the sleep period. On the basis of this information, RT and RR sequences have been automatically classified into two patterns, R and N. In this work, we propose a methodology to define new variables that are able to distinguish patients with hypertrophic cardiomyopathy (HCM) who later developed sudden cardiac death (SCD) from HCM patients without such episode during the follow-up. These variables are based on the instantaneous frequency calculation using time-frequency representation of the RT and RR signals previously classified into R and N patterns. In this study, three spectral bands have been considered: low-frequency band (LF, 0-0.07 Hz), mid-frequency band (MF, 0.07-0.15 Hz), and high-frequency band (HF, 0.15-0.45 Hz). Then a suitable combination of mean energy and mean frequency of the RT and RR signals in the MF and HF bands has allowed HCM patients with SCD to be discriminated from HCM patients without SCD (P < 0.001).