Sleep deprivation leads to cognitive impairments in humans and, if sustained for 2–3 weeks in rats, it is invariably fatal. It has been suggested that neural activity associated with waking, if it is not interrupted by periods of sleep, may damage brain cells through excitotoxic or oxidative mechanisms and eventually lead to cell death. To determine whether sustained waking causes brain cell degeneration, three parallel strategies were used. The presence and extent of DNA fragmentation was analyzed with the TUNEL technique on brain sections from rats sleep deprived for various periods of time (from 8 h to 14 days) and from their respective controls. Adjacent sections from the same animals were stained with a newly developed fluorochrome (Fluoro-Jade) specific for degenerating neurons. Finally, total RNA from the cerebral cortex of the same animals was used to determine whether the expression of several stress response genes and apoptosis-related genes is modified after sustained waking. In most long-term sleep deprived rats only a few scattered TUNEL positive nuclei (1–3) were found in any given brain section. The overall number, distribution, and morphology of TUNEL positive cells in long-term sleep deprived rats did not differ significantly from yoked controls, short-term sleep deprived rats, and sleep controls. No evidence of degenerating neurons as detected by Fluoro-Jade was found in any experimental group. mRNA levels of all the stress response genes and apoptosis-related genes tested did not differ between long-term sleep deprived rats and their yoked controls. These results argue against the hypothesis that sustained waking can significantly damage brain cells through excitotoxic or oxidative mechanisms and that massive cell death may explain the fatal consequences of sleep deprivation.