Autonomic cardiac activity during sleep has been widely studied. Research has mostly focused on cardiac activity between different sleep stages and wakefulness as well as between normal and pathological sleep. This work investigates autonomic activity changes during sleep onset in healthy subjects with long and short sleep onset latency (SOL). Polysomnography (PSG) and electrocardiography (ECG) were simultaneously recorded in 186 healthy subjects during a single night. Autonomic activity was assessed based on frequency domain analysis of RR intervals and results show that the analysis of RR intervals differs significantly between the short SOL and the long SOL groups. We found that the spectral power in the low frequency band (LF) was significantly higher in the long SOL group compared to the short SOL group in the first 10 minutes in bed intended to sleep. There was no significant difference for LF and the spectral power in the high frequency band (HF) 10 minutes before and after sleep onset between the two groups. Only in the short SOL group there was a significant increase in HF from the first 10 minutes in bed intended to sleep to 10 minutes before SO, while LF decreased significantly in both groups. The effect of time (5.5-min bin) on the heart rate variability (HRV) features around sleep onset showed that both LF and HF differed significantly during the period surrounding sleep onset only in the short SOL group.