Early fMRI studies comparing results from fMRI and electrophysiological experiments support the notion that the blood oxygen level-dependent (BOLD) signal reliably follows the spiking activity of an underlying neuronal population averaged across a small region in space and a brief period in time. However, more recent studies focusing on higher level cognitive factors such as attention and visual awareness report striking discrepancies between the fMRI response in humans and electrophysiological signals in macaque early visual areas. Four hypotheses are discussed that can explain the discrepancies between the two methods: (1) the BOLD signal follows local field potential (LFP) signals closer than spikes, and only the LFP is modulated by top-down factors, (2) the BOLD signal is reflecting electrophysiological signals that are occurring later in time due to feedback delay, (3) the BOLD signal is more sensitive than traditional electrophysiological methods due to massive pooling by the hemodynamic coupling process, and finally (4) there is no real discrepancy, and instead, weak but reliable effects on firing rates may be obscured by differences in experimental design and interpretation of results across methods.