Low-frequency temporal fluctuations of physiological signals (< 0.1 Hz), such as the respiration and cardiac pulse rate, occur naturally during rest and have been shown to be correlated with blood-oxygenation-level-dependent (BOLD) signal fluctuation. Such physiological signal modulations have been considered as sources of noise and their effects on BOLD signal are commonly removed in functional magnetic resonance imaging (fMRI) studies. However, possible neural correlates of the physiological fluctuations have not been considered nor examined in detail. In the present study we investigated this possibility by simultaneously acquiring electroencephalogram (EEG) with BOLD fMRI data, respiratory and cardiac waveforms in healthy human subjects at eyes-closed and eyes-open resting. We quantified the concurrent changes of the EEG power in the alpha frequency band, the respiration volume, and the cardiac pulse rate, then assessed the temporal correlations between alpha EEG power and physiological signal fluctuations. In addition, time-shifted time courses of alpha EEG power or physiological data were included as regressors to examine their correlations with the whole-brain BOLD fMRI signals. We observed a significant correlation between alpha EEG global field power and respiration, particularly at eyes-closed resting condition. Similar spatial patterns were observed between the correlation maps of BOLD with alpha EEG power and respiration, with negative correlations coinciding in the visual cortex, superior/middle temporal gyrus, inferior frontal gyrus, and inferior parietal lobule and positive correlations in the thalamus and caudate. Regressing out the physiological variations in the BOLD signal resulted in reduced correlation between BOLD and alpha EEG power. These results suggest a mutual link of neuronal origin between alpha EEG power, respiration, and BOLD signals.