The spatial and temporal response of the cerebral microcirculation to mild hypercapnia was investigated via two-photon laser-scanning microscopy. Cortical vessels, traversing the top 200 μm of somatosensory cortex, were visualized in α-chloralose-anesthetized Sprague–Dawley rats equipped with a cranial window. Intraluminal vessel diameters, transit times of fluorescent dextrans and red blood cells (RBC) velocities in individual capillaries were measured under normocapnic (PaCO2 = 32.6 ± 2.6 mm Hg) and slightly hypercapnic (PaCO2 = 45 ± 7 mm Hg) conditions. This gentle increase in PaCO2 was sufficient to produce robust and significant increases in both arterial and venous vessel diameters, concomitant to decreases in transit times of a bolus of dye from artery to venule (14%,P< 0.05) and from artery to vein (27%,P< 0.05). On the whole, capillaries exhibited a significant increase in diameter (16 ± 33%,P< 0.001,n= 393) and a substantial increase in RBC velocities (75 ± 114%,P< 0.001,n= 46) with hypercapnia. However, the response of the cerebral microvasculature to modest increases in PaCO2 was spatially heterogeneous. The maximal relative dilatation (range: 5–77%; mean ± SD: 25 ± 34%,P< 0.001,n= 271) occurred in the smallest capillaries (1.6 μm–4.0 μm resting diameter), while medium and larger capillaries (4.4 μm–6.8 μm resting diameter) showed no significant changes in diameter (P> 0.08,n= 122). In contrast, on average, RBC velocities increased less in the smaller capillaries (39 ± 5%,P< 0.002,n= 22) than in the medium and larger capillaries (107 ± 142%,P< 0.003,n= 24). Thus, the changes in capillary RBC velocities were spatially distinct from the observed volumetric changes and occurred to homogenize cerebral blood flow along capillaries of all diameters.