Measures of brain connectivity are currently subject to intense scientific and clinical interest. Multiple measures are available, each with advantages and disadvantages. Here, we study epilepsy patients with intracranial electrodes, and compare four different measures of connectivity. Perhaps the most direct measure derives from intracranial electrodes; however, this is invasive and spatial coverage is incomplete. These electrodes can be actively stimulated to trigger electrophysical responses to provide the first measure of connectivity. A second measure is the recent development of simultaneous BOLD fMRI and intracranial electrode stimulation. The resulting BOLD maps form a measure of effective connectivity. A third measure uses low frequency BOLD fluctuations measured by MRI, with functional connectivity defined as the temporal correlation coefficient between their BOLD waveforms. A fourth measure is structural, derived from diffusion MRI, with connectivity defined as an integrated diffusivity measure along a connecting pathway. This method addresses the difficult requirement to measure connectivity between any two points in the brain, reflecting the relatively arbitrary location of the surgical placement of intracranial electrodes. Using a group of eight epilepsy patients with intracranial electrodes, the connectivity from one method is compared to another method using all paired data points that are in common, yielding an overall correlation coefficient. This method is performed for all six paired-comparisons between the four methods. While these show statistically significant correlations, the magnitudes of the correlation are relatively modest (r (2) between 0.20 and 0.001). In summary, there are many pairs of points in the brain that correlate well using one measure yet correlate poorly using another measure. These experimental findings present a complicated picture regarding the measure or meaning of brain connectivity.