Background Gastrointestinal diseases are associated with substantial cost in health care. In times of the COVID-19 pandemic and further digitalization of gastrointestinal tract health care, mobile health apps could complement routine health care. Many gastrointestinal health care apps are already available in the app stores, but the quality, data protection, and reliability often remain unclear. Objective This systematic review aimed to evaluate the quality characteristics as well as the privacy and security measures of mobile health apps for the management of gastrointestinal diseases. Methods A web crawler systematically searched for mobile health apps with a focus on gastrointestinal diseases. The identified mobile health apps were evaluated using the Mobile Application Rating Scale (MARS). Furthermore, app characteristics, data protection, and security measures were collected. Classic user star rating was correlated with overall mobile health app quality. Results The overall quality of the mobile health apps (N=109) was moderate (mean 2.90, SD 0.52; on a scale ranging from 1 to 5). The quality of the subscales ranged from low (mean 1.89, SD 0.66) to good (mean 4.08, SD 0.57). The security of data transfer was ensured only by 11 (10.1%) mobile health apps. None of the mobile health apps had an evidence base. The user star rating did not correlate with the MARS overall score or with the individual subdimensions of the MARS (all P>.05). Conclusions Mobile health apps might have a positive impact on diagnosis, therapy, and patient guidance in gastroenterology in the future. We conclude that, to date, data security and proof of efficacy are not yet given in currently available mobile health apps.