The use of medicinal plants for the treatment of gastrointestinal disorders and ethnodiseases such as diarrhea, stomachache, dysentery, "empacho" (blockage), and bile is a common strategy among indigenous communities. It is estimated that approximately 34% of medicinal plants are used to treat diseases of the digestive tract. In Mexico, gastrointestinal infections caused by bacteria, parasites, or viruses represent one of the main causes of death in children in rural populations. Our objective was to document the use of medicinal plants used by the indigenous groups of Oaxaca, Mexico, for the treatment of gastrointestinal disorders, based on previous studies, experiences, and field observations in indigenous communities and supplemented with bibliographic references. In Oaxaca, there are 16 indigenous groups, the largest being the speakers of the Zapoteco, Mixteco, Mazateco, Mixe, Chinanteco, Amuzgo, Tacuate, Chatino, and Cuicateco languages. In this review of the medicinal plants used for gastrointestinal disorders, 186 species were grouped into 147 genera and 71 botanical families, among which the largest number of species belonged to Asteraceae (29), Fabaceae (15), Euphorbiaceae (9), Solanaceae (9), and Lamiaceae (9). Different pharmacological studies showed potential for preventing microbial and fungal pathogens that cause gastrointestinal disease.