Recurrent abdominal pain (RAP) is the cause of disruption of daily activities/missed school days, overutilization of healthcare, unnecessary surgeries, and anxiety in 10 to 15% of children. Its etiology is not clearly understood, however, the success of several clinical protocols suggests that autonomic disregulation is a factor. This study compared autonomic activity, including heart rate variability (HRV), in forty-one children between the ages of five and seventeen years old with and without RAP. Pain histories and demographic information was obtained along with pain severity and frequency information. Psychophysiological measures included Electrocardiograph (ECG), Pneumograph (PNG), and Electrodermograph (EDG) monitoring. Approximately 45 minutes of psychophysiological data was obtained for each participant during five conditions: baseline, paced breathing, serial sevens, recovery, and reading. Results revealed that children with RAP failed to recover from the stress condition and that sympathetic stimulation occurred without vagal withdrawal.