Eur J Clin Invest 2012 ABSTRACT: Background and Methods  Low frequency oscillations (LFO) of cerebral vessels are believed to reflect cerebral autoregulation. We investigated day-to-day and hemispheric variations in 0·1 Hz LFO with near infrared spectroscopy (NIRS) and transcranial Doppler (TCD) to determine phase shift and gain of oxygenated haemoglobin (oxyHb) and the velocity of the middle cerebral artery (Vmca) to the arterial blood pressure (ABP). The direct left-right phase shifts of oxyHb and Vmca were also assessed. We examined 44 healthy volunteers by simultaneous recordings of ABP, oxyHb and Vmca during spontaneous and paced breathing at 6 breaths per minute on two separate days. Results  The variation between hemispheres had a prediction interval (PI) of ±39° for ABP-oxyHb phase shift and ±69% for gain. ABP-Vmca showed ±57° PI phase shift and ±158% PI for gain. The variation from day to day showed ±61° PI for ABP-oxyHb phase shift and ±297% PI for gain. ABP-Vmca showed ±45° PI phase shift and ±166% PI for gain. We found a linear relation between phase shift of oxyHb and Vmca at paced breathing (P = 0·0005), but not at rest (P = 0·235). Conclusion  Our results show that LFO phase shift ABP-oxyHb may be used as a robust measurement of differences in autoregulation between hemispheres and over time. In addition, we found a strong relation between oxyHb and Vmca during paced breathing. Gain showed too large variation for clinical use, as the SD was up to 100-fold of mean values.