Sleep disturbances manifesting as insomnia, daytime sleepiness, fatigue, and other symptoms are frequently found in patients with end-stage renal disease that is being treated with dialysis. Many factors, including neurosis, uremic symptoms, dialysis drugs, and sleep-wake rhythms have been suggested as potential causes for these sleep disturbances. We examined sleep apnea/hypopnea and heart rate variability (HRV) reflecting autonomic activity in hemodialysis patients on their hemodialysis and non-hemodialysis days using a home medical care device (Morpheus C, TEIJIN). Eleven hemodialysis patients and 14 healthy adults were enrolled in this study. We calculated the number of apnea/hypopnea episodes per hour (apnea/hypopnea index: AHI) and HRV (percentage of R-R intervals that differ by at least 50 ms from the previous interval: pNN50, very low frequency: VLF, low frequency: LF, high frequency: HF and LF/ HF). There was no significant difference in the AHI between hemodialysis and non-hemodialysis days. The heart rate in hemodialysis patients on non-hemodialysis days was significantly higher than in the controls, whereas the pNN50 was significantly lower in hemodialysis patients on non-hemodialysis days than in the controls. Although VLF was significantly lower in hemodialysis patients on non-hemodialysis days compared to the controls, there were no significant differences in LF, HF or LF/HF between the two groups. Hemodialysis itself might not be an important contributing factor in sleep-related breathing disturbances. The simultaneous analysis of HRV reflecting autonomic activity and sleep-disordered breathing on both hemodialysis and non-hemodialysis days provides important information.