BACKGROUND: Functional magnetic resonance imaging (fMRI) is one of the most important neuroimaging techniques; nevertheless, the acoustic noise of the MR scanner is unavoidably linked to the process of data acquisition. We hypothesized that the auditory noise of the scanner has an effect on autonomic activity. METHODS: We measured heart rate variability (HRV) while exposing 30 healthy subjects to fMRI noise. In doing so, we demonstrated an increase in parasympathetic nervous system (PNS) activity compared to silence and white noise and a decrease in sympathetic nervous system (SNS) activity compared to white noise. CONCLUSIONS: The influence of MR scanner noise on the autonomic nervous system should be taken into account when performing fMRI experiments.