The book opens with a Kentucky farmer named Arthur Shelby facing the loss of his farm because of debts. Even though he and his wife Emily Shelby believe that they have a benevolent relationship with their slaves, Shelby decides to raise the needed funds by selling two of them--Uncle Tom, a middle-aged man with a wife and children, and Harry, the son of Emily Shelby's maid Eliza--to Mr. Haley, a coarse slave trader. Emily Shelby is averse to this idea because she had promised her maid that her child would never be sold; Emily's son, George Shelby, hates to see Tom go because he sees the man as his friend and mentor.

When Eliza overhears Mr. and Mrs. Shelby discussing plans to sell Tom and Harry, Eliza determines to run away with her son. The novel states that Eliza made this decision because she fears losing her only surviving child (she had already miscarried two children). Eliza departs that night, leaving a note of apology to her mistress.

As Tom is sold, Mr. Haley takes him to a riverboat on the Mississippi River and from there Tom is to be transported to a slave market. While onboard, Tom meets Eva, an angelic little white girl and quickly they become friends. Eva falls into the river and Tom dives into the river to save her life. Being grateful to Tom, Eva's father Augustine St. Clare buys him from Haley and takes him with the family to their home in New Orleans. Tom and Eva begin to relate to one another because of the deep Christian faith they both share.