Chronic Fatigue Syndrome (CFS) is a disease characterized by high levels of daytime fatigue. Complaints such as unrefreshing sleep and insomnia are common. Polygraphic studies of sleep in CFS patients have found evidence of disturbed sleep, but controls in these studies were often not adequate to evaluate differences specific to CFS. Watson, et al. [1] and Ball, et al. [2] used a co-twin control design to eliminate virtually all sources of confounding variance and found a small difference between levels of Stage 2 sleep (lower in CFS) and Stage 3 sleep (higher in CFS), where CFS ill twins showed a higher level of sleep complaint than the healthy twins which was not reflected in their sleep physiology. The current study will apply more sensitive measures of sleep EEG to these data to examine differences more closely. A cotwin control study was performed on 10 pairs of identical twins discordant for CFS. Data from the second sleep night were analyzed using fast-fourier analysis (FFT) and finally measures of slow-wave activity (SWA). Data for NREM periods was analyzed. There was a significant interaction in SWA for Twin x NREM period for the first 2 NREM periods with the healthy twins having more SWA in the first NREM period and less in the second NREM period. While overall SWA activity did not differentiate the groups, the distribution of SWA in the first 2 NREM periods could be associated with the experience of unrefreshing sleep. Typically, SWA in the first NREM period is associated with deep restorative sleep. Lower SWA in NREMP 1 in the ill CFS twins suggests that this process is compromised resulting in the experience of less refreshing sleep.