Disturbed sleep is one of the most common symptoms reported by people diagnosed with chronic fatigue syndrome (CFS). The biopsychosocial causes and consequences are poorly understood. The hypothalamic-pituitary-adrenal (HPA) axis is a diurnal hormone cascade responsible for regulating the response to stress; it influences energy metabolism and immune functioning and has been shown to be differently regulated in CFS. We hypothesise that measures of objective sleep and HPA axis function have a bidirectional relationship and have aetiopathogenic significance in CFS. In this preliminary study, polysomnography (PSG) – an all-night recording of sleep physiology – was conducted and analysed for 11 CFS patients. PSG was recorded over three consecutive nights in the homes of the participants. The 3-night protocol improves reliability and allows habituation to the cumbersome equipment. HPA axis function was estimated by collecting saliva samples at 15 minute intervals for 1 hour from wakening, at 4 pm and 11 pm for the 3 days following the sleep recordings. We used a linear mixed-effects modelling approach to examine variation in PSG parameters in patients with CFS as a function of cortisol, Chalder fatigue scale constructs and demographic variables (age, gender, body mass index (BMI), weight and duration of disease). Evidence of the first-night effect in CFS patients was confirmed with more stage-1 and less stage-3 sleep on the first night. We found statistically significant associations between cortisol levels and the duration of wake-periods, and the latency to rapid eye movement (REM) sleep. Determining cause and effect was not possible in this study but the results may be caused by a bidirectional relationship between the PSG parameters and cortisol, with each perpetuating the other.