The study of bioelectric and biomagnetic activity in the human gastrointestinal (GI) tract is of great interest in clinical research due to the proven possibility to detect pathological conditions thereof from electric and magnetic field recordings. The magnetogastrogram (MGG) and magnetoenterogram (MENG) can be recorded using superconducting quantum interference device (SQUID) magnetometers, which are the most sensitive magnetic flux-to-voltage converters currently available. To address the urgent need for powerful acquisition and analysis software tools faced by many researchers and clinicians in this important area of investigation, an integrative and modular computer program was developed for the acquisition, processing and analysis of GI SQUID signals. In addition to a robust hardware implementation for efficient data acquisition, a number of signal processing and analysis modules were developed to serve in a variety of both clinical procedures and scientific investigations. Implemented software features include data processing and visualization, waterfall plots of signal frequency spectra as well as spatial maps of GI signal frequencies. Moreover, a software tool providing powerful 3D visualizations of GI signals was created using realistic models of the human torso and internal organs.