An access system includes a proximal handle, an overtube coupled to the handle, and an endoscope port extending through handle and overtube sized for receiving an endoscope therethrough. The overtube includes anatomic wall securing system that secures a distal portion of the overtube within a hole in the anatomic wall. The overtube is provided with a shaped distal portion or a controllably shapeable distal portion that aids in directing an endoscope inserted through the port to a particular location within the peritoneal cavity. The access system includes a system for insufflating/deflating the peritoneal space separately from the body cavity accessible via a natural orifice. The access system includes a closure system to cinch closed the hole made in the anatomical wall after the access system has been removed from the hole. Methods are provided for inserting the access system through the anatomical wall to perform intra-abdominal surgery.