Electrical activity in the gastrointestinal system produces magnetic fields that may be measured with superconducting quantum interference device magnetometers. Although typical magnetometers have detection coils that measure a single component of the magnetic field, gastric and intestinal magnetic fields are vector quantities. We recorded gastric and intestinal magnetic fields from nine abdominal sections in nine normal human volunteers using a vector magnetometer that measures all three Cartesian components of the magnetic field vector. A vector projection technique was utilized to separate the magnetic field vectors corresponding to gastric and intestinal activity. The gastric magnetic field vector was oriented in a cephalad direction, consistent with previously observed data, and displayed oscillatory characteristics of gastric electrical activity (f = 3.03 +/- 0.18 cycles/min). Although the small bowel magnetic field vector showed no consistent orientation, the characteristic frequency gradient of the small bowel electrical activity was observed. Gastric and intestinal magnetic field vectors were oriented in different directions and were thus distinguished by the vector projection technique. The observed difference in direction of gastric and intestinal magnetic field vectors indicates that vector recordings dramatically increase the ability to separate physiological signal components from nonphysiological components and to distinguish between different physiological components.