While Tom Sawyer’s hometown of St. Petersburg is fictional, many elements of Mark Twain’s childhood in Hannibal, Missouri, were incorporated into the story. Note that Mark Twain is a pen name, and the author’s given name was Samuel Clemens. The Clemens’ family home was constructed in 1843 or 1844, and the Tom Sawyer is set in the 1840s. Samuel Clemens lived in a two-story frame house, and there is historical photographic evidence of him standing in front of his childhood home. The photograph indicates the house was painted white or beige and had shutters. Tom Sawyer's house is a one-story Acadian-style home with green shutters, and it has a porch (which the Clemens family home lacks); in the novel, Tom hides under the floorboards of the porch in order to avoid chores given to him by Aunt Polly.
Mark Twain/Samuel Clemens based the cave in The Adventures of Tom Sawyer on a real cave located South of Hannibal, Missouri. Before the novel's publication, it was called McDowell’s Cave and was owned by Dr. Joseph Nash McDowell, who studied corpse decomposition and stored bodies in the temperate cave. McDowell was a larger-than-life medical professional in Twain’s hometown and likely inspired the graveyard scene and the character of Dr. Robinson, who hires Injun Joe and Muff Porter to dig up a body. In his Autobiography, Mark Twain describes how children would explore the cave and tell ghost stories around the body of McDowell’s daughter, which was suspended within a copper tube filled with alcohol; this provides an undoubtedly interesting and macabre backstory to the novel. Chapter 29 describes McDougal’s Cave:
Walled by Nature with solid limestone that was dewy with a cold sweat. It was romantic and mysterious to stand here in the deep gloom and look out upon the green valley shining in the sun . . . McDougal's cave was but a vast labyrinth of crooked aisles that ran into each other and out again and led nowhere. It was said that one might wander days and nights together through its intricate tangle of rifts and chasms, and never find the end of the cave . . . No man "knew" the cave. That was an impossible thing. Most of the young men knew a portion of it, and it was not customary to venture much beyond this known portion.
The cave that inspired this setting in the novel is similarly located within a hillside and made of limestone. It also contains the same narrow and winding passages as described in the book. The narrator’s perspective in which Twain describes the mysterious cave can be viewed as reminiscent of Clemens’ own childhood impressions of McDowell’s cave.