Spatial specificities of the calcium‐dependent synaptic activity, hemodynamic‐based blood oxygenation level‐dependent (BOLD) and cerebral blood flow (CBF) fMRI were quantitatively compared in the same animals. Calcium‐dependent synaptic activity was imaged by exploiting the manganese ion (Mn⁺⁺) as a calcium analog and an MRI contrast agent at 9.4 T. Following forepaw stimulation in α‐chloralose anesthetized rat, water T₁ of the contralateral forepaw somatosensory cortex (SI) was focally and markedly reduced from 1.99 ± 0.03 sec to 1.30 ± 0.18 sec (mean ± SD, N = 7), resulting from the preferential intracellular Mn⁺⁺ accumulation. Based on an in vitro calibration, the estimated contralateral somatosensory cortex [Mn⁺⁺] was ∼100μM, which was 2–5‐fold higher than the neighboring tissue and the ipsilateral SI. Regions with the highest calcium activities were localized around cortical layer IV. Stimulus‐induced BOLD and CBF changes were 3.4 ± 1.6% and 98 ± 33%, respectively. The T₁ synaptic activity maps extended along the cortex, whereas the hemodynamic‐based activation maps extended radially along the vessels. Spatial overlaps among the synaptic activity, BOLD, and CBF activation maps showed excellent co‐registrations. The center‐of‐mass offsets between any two activation maps were less than 200 μm, suggesting that hemodynamic‐based fMRI techniques (at least at high field) can be used to accurately map the spatial loci of synaptic activity. Magn Reson Med 43:383–392, 2000. © 2000 Wiley‐Liss, Inc.