Apparatus and methods are provided for mapping out endoluminal gastrointestinal surgery, including endoluminal gastric reduction. Mapping is achieved by locally marking the interior of the gastrointestinal lumen at specified locations. In some variations, mucosectomy and/or mucosal ablation are performed to map out endoluminal GI surgery, to facilitate direct endoluminal engagement of underlying muscularis tissue and/or to initiate a wound healing response. Specialized apparatus may be provided to achieve desired spacing and/or positioning of tissue markings, as well as to actually form the markings. Methods of using apparatus of the present invention are provided.