Diffuse optical tomography (DOT) is a portable functional neuroimaging technique that is able to simultaneously measure both oxy- and deoxyhemoglobin responses to brain activity. Herein, we demonstrate a technique for mapping functional connections in the brain by measuring the spatial distribution of temporal correlations in resting brain activity. Simultaneous DOT imaging over the motor and visual cortices yielded robust correlation maps reproducing the expected functional neural architecture. These functional connectivity methods will have utility in certain populations, such as those who are unconscious or very young, who have difficulty performing the behaviors required in traditional task-based functional neuroimaging paradigms.