This study aims to improve the method used to produce cerebrovascular reactivity (CVR) maps by MRI. Previous methods have used a standard boxcar presentation of carbon dioxide (CO(2)). Here this is replaced with a sinusoidally modulated CO(2) stimulus. This allowed the use of Fourier analysis techniques to measure both the amplitude and phase delay of the BOLD CVR response, and hence characterize the arrival sequence of blood to different regions of the brain. This characterization revealed statistically significant relative delays between regions of the brain (ANOVA < 0.0001). In addition, post hoc comparison showed that the frontal (P < 0.001) and parietal (P = 0.004) lobes reacted earlier than the occipital lobe.