We developed a cross-over study design with two interventions in randomized order to compare the effects of sleep fragmentation and partial sleep restriction on cardiac autonomic tone. Twenty male subjects (40.6 +/- 7.5 years old) underwent overnight polysomnography during 2 weeks, each week containing one undisturbed baseline night, one intervention night (either sleep restriction with 5 h of sleep or sleep fragmentation with awakening every hour) and two undisturbed recovery nights. Parameters of heart rate variability (HRV) were used to assess cardiac autonomic modulation during the nights. Sleep restriction showed significant higher heart rate (p = 0.018) and lower HRV-pNN50 (p = 0.012) during sleep stage N1 and lower HRV-SDNN (p = 0.009) during wakefulness compared to the respective baseline. For HR and SDNN there were recovery effects. There was no significant difference comparing fragmentation night and its baseline. Comparing both intervention nights, sleep restriction had lower HRV high frequency (HF) components in stage N1 (p = 0.018) and stage N2 (p = 0.012), lower HRV low frequency (LF) (p = 0.007) regarding the entire night and lower SDNN (p = 0.033) during WASO during sleep. Sleep restriction increases sympathetic tone and decreases vagal tone during night causing increased autonomic stress, while fragmented sleep does not affect cardiac autonomic parameters in our sample.