BACKGROUND: It is increasingly popular to use heart-rate variability (HRV) to tailor training for athletes. A time-efficient method is HRV assessment during deep sleep. AIM: To validate the selection of deep-sleep segments identified by RR intervals with simultaneous electroencephalography (EEG) recordings and to compare HRV parameters of these segments with those of standard morning supine measurements. METHODS: In 11 world-class alpine skiers, RR intervals were monitored during 10 nights, and simultaneous EEGs were recorded during 2-4 nights. Deep sleep was determined from the HRV signal and verified by delta power from the EEG recordings. Four further segments were chosen for HRV determination, namely, a 4-h segment from midnight to 4 AM and three 5-min segments: 1 just before awakening, 1 after waking in supine position, and 1 in standing after orthostatic challenge. Training load was recorded every day. RESULTS: A total of 80 night and 68 morning measurements of 9 athletes were analyzed. Good correspondence between the phases selected by RR intervals vs those selected by EEG was found. Concerning root-mean-squared difference of successive RR intervals (RMSSD), a marker for parasympathetic activity, the best relationship with the morning supine measurement was found in deep sleep. CONCLUSION: HRV is a simple tool for approximating deep-sleep phases, and HRV measurement during deep sleep could provide a time-efficient alternative to HRV in supine position.