Cortical blood flow was probed via the motion of red blood cells (RBCs) in individual capillaries that lay as much as 600 μm below the pia matter of primary somatosensory cortex in rat. The flow was quite variable, with a speed of 0.8±0.5 mm/s (mean±S.D.) and a flux of 60±40 RBC/s, averaged over all capillaries and over time. The fluctuations in the flow were dominated by a spectral band near 0.1 Hz. This band coincides with the spectral band of fluctuations previously seen across whole capillary beds with optical [Neuroimage 4 (1996) 183] and fMRI [Mag. Reson. Med. 37 (1997) 511] imaging techniques. Time-locked increases in the flow of red blood cells (RBCs) within individual capillaries were observed in response to stimulation of multiple vibrissae at natural levels of deflection. The magnitude of the stimulus-evoked change in speed was, at most, equal to 20% of the basal speed. This change is comparable to the level of the fluctuations in speed seen in single capillaries. Thus, changes in flow evoked by natural stimuli are largely masked by basal fluctuations. In toto, the results of our study suggest that fluctuations at the level of the microvasculature limit the sensitivity of brain imaging techniques, at least at low frequencies.