Different EEG-vigilance stages from full alertness to sleep onset can be separated during rest. Also fMRI research recently focused on the resting condition and identified several resting state networks. In order to deepen the understanding of different levels of global brain function from relaxed wakefulness to sleep onset the association between EEG-vigilance stages and BOLD signals was analysed. EEG-vigilance stages were attributed to consecutive 3-sec-EEG-segments by an algorithm using topographic and spectral information. Results of the classification were validated by analysing the heart rates during the different brain states. Vigilance stages served as regressors for the analysis of the simultaneously acquired fMRI data. Additionally resting state networks were derived from the fMRI data using independent component analysis (ICA). Also vigilance associated brain activity revealed by EEG-based standardized low resolution tomography (sLORETA) was compared to the results of the fMRI analysis. Results showed increased BOLD signal in the occipital cortex, the anterior cingulate cortex, the frontal cortex, the parietal cortices and the temporal cortices and decreasing BOLD signals in the thalamus and the frontal cortex for declining vigilance stages (A2, A3, B1, B2/B3) in comparison to the high vigilance stage A1. Resting state networks revealed a spatial overlap with the vigilance stage associated BOLD maps in conjunction analyses. sLORETA showed increased neuroelectric alpha activity at the occipital cortex comparable to occipital BOLD signal decreases when comparing stage A with stage B. Different EEG-vigilance stages during rest are associated with pronounced differences of BOLD signals in several brain areas which partly correspond to the resting state networks. For cognitive fMRI-research it therefore seems important to pay attention to vigilance switches in order to separate vigilance associated BOLD signal changes from those specifically related to cognition.