An accurate and reliable localization of endoluminal gastrointestinal (GI) lesions is crucial, particularly during minimally invasive surgery. As an extreme consequence, a misdetected GI lesion can lead to the resection of the wrong segment, especially in colorectal surgery. A preoperative endoscopic marking is recommended in case of GI lesions, which are expected to be difficult to detect from the serosal side. In clinical practice, three preoperative endoscopic marking methods are currently used: India ink, SPOT™, and endoclips with intraoperative fluoroscopy. All of them have substantial limitations. This has encouraged research on alternative solutions. In the current systematic review, animal and clinical studies about alternative preoperative endoscopic marking methods of GI lesions were analyzed using the PRISMA (Preferred Reporting Items for Systematic Reviews and Meta-Analyses) guidelines. Thirty studies were found using PubMed/MEDLINE, EMBASE/Ovid, and the Cochrane Library for the qualitative analysis. Although several smart solutions have been proposed and tested successfully, all of them seem to have a substantial drawback related either to scarce stability on the marking site or potential spreading on the bowel wall or diffusion into the surgical planes.