In humans, the location of brain regions responsible for mediating the ventilatory response to CO2 remains unknown. Most of the available knowledge has been derived from animal studies or from pathophysiological correlations in patients presenting altered control of breathing. Magnetic resonance imaging at a specific pulse sequence designed to assess changes in brain tissue microcirculation was performed in 11 healthy volunteers, during steady-state conditions, while breathing 100% O2 or 5% CO2-95% O2. In one subject, 10% CO2-90% O2 was employed to examine a dose-response effect. Significant changes in image signal intensity consistently occurred in ventral and dorsal regions of medullary structures as well as in the midline pons and ventral cerebellum. These responses appeared to be dose dependent and reproducible. Magnetic resonance imaging revealed patterns of activation in brain stem and cerebellar regions during hypercapnic ventilatory challenge. These areas may underlie mechanisms for mediating the response to chemoreceptor activation.