Many children with autism spectrum disorder (ASD) have gastrointestinal (GI) problems and associated fecal incontinence, constipation, and diarrhea. We describe the design and operation of a computer-assisted health monitoring system for tracking and recording bowel movements at a residential school. Implementation integrity of the system by care providers was 100% for six targeted students with ASD and GI difficulties. The utility, objectives, and effectiveness of the system were rated positively by supervisory professionals, parents, and GI physicians. Our discussion focuses on the advantages of computer-assisted data recording and instrumentation technology for documenting health measures such as bowel movement frequency and quality in children with ASD.