The relationship between the time course of cortical temperature (TCRT) and sleep-wake alternation was investigated by correlation analyses and a computer simulation. The data for these analyses were collected in 10 rats in a 4-day experiment (LD 12:12), during which vigilance states and TCRT were determined for consecutive 8-sec epochs. On day 1 baseline recordings were obtained; on day 2 the animals were sleep-deprived; and days 3 and 4 served as recovery days. The correlation analyses revealed that the alternation of sleep and waking accounted for 84% of the variance of TCRT when analyzed for hourly intervals. The residual variance displayed a 24-hr periodicity with an amplitude of 0.15 degrees C. Similar results were obtained in a separate data set of a 2-day experiment, which consisted of a baseline day (LD 12:12) and a day with constant darkness. The periodicity of the residual variance of TCRT can therefore be considered to represent the circadian temperature rhythm not masked by the vigilance states. In the computer simulation, the time course of TCRT was simulated on the basis of the sequence of the vigilance states with an 8-sec time resolution. It was assumed that TCRT increases during waking and rapid-eye-movement (REM) sleep according to an exponential saturating function, and decreases exponentially during non-REM sleep. The simulations could account for 88-93% of the variance of TCRT. We conclude that in the rat, the major part of the variation of TCRT is accounted for by vigilance states, whereas a minor part can be attributed to a direct effect of the circadian pacemaker.