Culkin was the fourth of seven children born to Christopher "Kit" Culkin and Patricia Brentrup. His father is a former stage actor, and his mother, a native of North Dakota, worked as a road traffic controller in Sundance, Wyoming. Culkin was raised Catholic with his six siblings: Shane, Dakota, Macaulay, Quinn, Christian, and Rory. He had an older half-sister, Jennifer Adamson, from his father's previous relationship. Actress Bonnie Bedelia is his paternal aunt. Culkin has German, Irish, and Norwegian ancestry.
For the first nine years of his life, Culkin and his family lived in a railroad apartment in Yorkville and struggled financially. The tenement was "barely suitable for a couple," Culkin explained to Vanity Fair. "It was just a hallway, and there were no separating doors, except for the bathroom, which didn't have a lock. [His parents] raised seven kids in that apartment—for years! They just kept bringing babies home to this little space." Because his father served as a sacristan at the St. Joseph's Church of Yorkville, Culkin attended its Catholic school for free until the third grade. He then studied theater, film and television at the Professional Children's School, but dropped out during his senior year of high school.
Culkin was "loved unconditionally" by his mother, and considers her to be his only parent. He was neglected by his father throughout his childhood and only remembers him as being a "constant, unwelcome presence" in the household. His mother handled all of the children's necessities while balancing night shifts as a telephone operator for a theatrical casting agency. According to the family's longtime talent manager, Emily Gerson Saines, his mother maintained "strong family values, like the family having a meal together, the Christmas tree, Thanksgiving. These are all important things to [Brentrup], and she instilled that in her kids." After living together for more than twenty years, Culkin's parents separated in March 1995. Brentrup was awarded sole custody of five of their seven children following a two-year, highly publicized custody battle. Culkin maintained a "great" relationship with his mother, but has been estranged from his father since.