Spatiotemporally structured noise, such as physiological noise, is a potential source of artifacts in functional magnetic resonance imaging (fMRI) and is the main limiting factor for the detection of small blood oxygen level-dependent (BOLD) signal variations. fMRI was employed to detect low-frequency BOLD signal fluctuations. which are thought to be related to spontaneous neuronal activity in the resting human brain. The sensitivity to noise, that is, signal variations of nonBOLD origin, was investigated for two- (2D) and three-dimensional (3D) imaging techniques. Incomplete relaxation between subsequent scans increases the level of temporally and spatially correlated signal variations originating from physiological and/or systemic noise. Although inflow effects are suspected to be reduced in 3D echo-planar imaging (EPI) compared with multi-slice 2D EPI, the noise level was higher in the 3D technique. The noise level in 3D fMRI experiments was significantly increased by instabilities of the transverse steady-state magnetization as the repetition time was of the order of T-2. By implementing radiofrequency spoiling, temporal signal fluctuations and erroneous inter-regional correlation in connectivity maps were diminished to a level present in data sets acquired with 2D EPI. Copyright (c) 2005 John Wiley & Sons, Ltd.