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Nausea is a commonly occurring symptom typified by epigastric discomfort with the urge to vomit. To date, the brain circuitry underlying the autonomic nervous system response to nausea has not been fully understood. Functional MRI (fMRI), together with a point process adaptive recursive algorithm for computation of the high-frequency (HF) index of heart rate variability (HRV) was combined to evaluate the brain circuitry underlying autonomic nervous system response to nausea. Alone, the point process analysis revealed increasing sympathetic and decreasing parasympathetic response during nausea with significant increased heart rate (HR) and decreased HF. The combined HRV-fMRI analysis demonstrated that the fMRI signal in the medial prefrontal cortex (MPFC) and pregenual anterior cingulate cortex (pgACC), regions of higher cortical functions and emotion showed a negative correlation at the baseline and a positive correlation during nausea. Overall, our findings confirm a sympathovagal shift (toward sympathetic) during nausea, which was related to brain activity in regions associated with emotion and higher cognitive function.