The Superconducting QUantum Intewrference Device (SQUID) magnetometer can non-invasively detect the magnetic fields created by the Basic Electrical Rhythm (BER) of the Gastrointestinal Tract (GIT). Using anesthetized adult male New Nealand rabbits we recorded signals from two isolated bowel segments at the same time, before and after ischemia was induced in either one or both bowel segments. The dominant frequency peaks for each period of recording were determined using autoregressive (AR) spectral analysis. There was a significant fall in the BER frequency in the ischemic segment from 11.8 ± 0.9 to 7.8 ± 0.6 cycles per minute (cpm), while there was no change in the normal bowel. It was possible for two observers (LAB, WOR) who were blinded to the preparation, to identify which bowel segment was ischemic. The results of this experiment demonstrate the ability of the SQUID magnetometer to non-invasively detect and differentiate signals from normal and ischemic bowel sources. © 1997 IEEE