In this study we set out to understand is sleep fragmentation affects the cardiovascular regulation and circadian variability of core body temperature more or less than sleep deprivation. 50 healthy men (age 29.0+/-3.1 years; BMI 24.3+/-2.1 kg/m(2)) participated in a 3-day study that included one adaptative night and one experimental night involving randomization to: sleep deprivation (SD) and sleep fragmentation (SF). The evaluation included hemodynamic parameters, measures of the spectral analysis of heart rate and blood pressure variability, and the sensitivity of arterial baroreflex function. Core body temperature (CBT) was measured with a telemetric system. SF affects heart rate (61.9+/-5.6 vs. 56.2+/-7.6, p<0.01) and stroke index (52.7+/-11.1 vs. 59.8+/-12.2, p<0.05) with significant changes in the activity of the ANS (LF-sBP: 6.0+/-5.3 vs. 3.4+/-3.7, p<0.05; HF-sBP: 1.8+/-1.8 vs. 1.0+/-0.7, p<0.05; LF-dBP: 5.9+/-4.7 vs. 3.5+/-3.2, p<0.05) more than SD. Post hoc analysis revealed that after SD mean value of CBT from 21:30 to 06:30 was significantly higher compared to normal night's sleep and SF. In healthy men SF affects the hemodynamic and autonomic changes more than SD. Sympathetic overactivity is the proposed underlying mechanism.