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Since its first therapeutic application in ophthalmology in the 1980s, botulinum toxin has continued to attract interest, with a steadily growing number of clinical indications. In gastroenterology, although botulinum toxin injections are used to treat a variety of diseases, no marketing authorization has yet been granted for these uses. Botulinum toxin injections can be used to treat esophageal diseases, including upper esophageal sphincter dysfunction, achalasia, and nonspecific motility disorders such as hypercontractile esophagus or isolated hypertensive lower esophageal sphincter. Gastroparesis is also a current indication for (intra-pyloric) botulinum toxin injections, as are anismus, anal fissures and, more recently, anal incontinence (rectal injections). Although the level of scientific evidence supporting these indications is not always very high, botulinum toxin injections are an interesting therapeutic option, as they are simple to perform and associated with low morbidity.