Recently, we reported on the unusual "switch-off" of respiratory sinus arrhythmia (RSA) by analyzing heart rate (HR) beat-to-beat interval (RRI) signals and respiration in five subjects during a potentially anxiety-provoking first-time functional magnetic resonance imaging (fMRI) scanning with slow spontaneous breathing waves (Rassler et al., 2018). This deviation from a fundamental physiological phenomenon is of interest and merits further research. Therefore, in this study, the interplay between blood-oxygen level-dependent (BOLD) activity in the cerebellum/brain stem, RRI, and respiration was probed. Both the cardiovascular and the respiratory centers are located in the medulla oblongata and pons, indicating that dominant slow rhythmic activity is present in the brain stem. The recording of BOLD signals provides a way to investigate associated neural activity fluctuation in the brain stem. We found slow spontaneous breathing waves associated with two types of slow BOLD oscillations with dominant frequencies at 0.10 and 0.15 Hz in the brain stem. Both BOLD oscillations were recorded simultaneously. One is hypothesized as vessel motion-based phenomenon (BOLDv) associated with the start of expiration; the other one as pattern associated with neural activity (BOLDn) acting as a driving force for spontaneous inspiration and RRI increase (unusual cessation of RSA) about 2-3 s after BOLDv. This time delay of 2-3 s corresponds to the neurovascular coupling time.