A fully automated computer-based sleep scoring system is described and validated for use in rats. The system was designed to emulate visual sleep scoring by using the same basic features of the electroencephalogram (EEG) and electromyogram (EMG), and a similar set of decision-making rules. State indices are calculated for each 5s epoch by combination of amplitudes (microVrms) of 6 filtered EEG frequency bands (EEGlo, d.c.-1.5Hz; delta, 1.5-6Hz; theta, 6-9Hz; alpha, 10.5-15Hz; beta, 22-30Hz; gamma, 35-45Hz; Sigma(EEG)=delta+theta+alpha+beta+gamma) and EMG (10-100Hz) yielding dimensionless ratios: WAKE-index=(EMGxgamma)/theta; NREM-index=(deltaxalpha)/gamma(2); REM-index=theta(3)/(deltaxalphaxEMG); artifact-index=[(2xEEG(lo))+beta]*(gamma/Sigma(EEG)). The index values are re-scaled and normalized, thereby dispensing with the need for animal-specific threshold values. The system was validated by direct comparison with visually scored data in 9 rats. Overall, the computer and visual scores were 96% concordant, which is similar to inter-rater agreement in visual scoring. False-positive error rate was <5%. A re-test protocol in 7 rats confirmed the long-term stability of the system in studies lasting 5 weeks. The system was implemented and further validated in a study of sleep architecture in 7 rats under a 12:12h LD cycle.