Aniston was born in Sherman Oaks, California, the daughter of actor John Aniston and actress Nancy Dow (1936-2016). Her father is Greek, while her mother was born in New York City. One of her maternal great-grandfathers was anItalian immigrant, and her mother's other ancestry includes English, Irish, Scottish, and a small amount of Greek. Aniston has two half-brothers, John Melick, her older maternal half-brother, and Alex Aniston, her younger paternal half-brother. Aniston's godfather was actor Telly Savalas, one of her father's best friends.
As a child, Aniston lived in Greece for a year with her family. They then moved to Eddystone, Pennsylvania, where they lived with her grandmother Stella Anastassakis in a three-bedroom home. While living in Eddystone, Aniston was enrolled at a local elementary school. She and her family later moved to New York City. Despite her father's television career, Aniston was discouraged from watching TV, though she found ways around the prohibition. When she was six, she began attending a Waldorf school. Her mother and father split up when she was nine years old. Her father is best known for his role as Victor Kiriakis on the NBC daytime drama Days of Our Lives, which he originated in 1985. Her mother appeared in two 1960s TV series, The Wild Wild West and The Beverly Hillbillies.
Having discovered acting at age 11 at the Waldorf school, Aniston enrolled in and graduated from Manhattan's Fiorello H. LaGuardia High School of Music & Art and Performing Arts, where she joined the school's drama society. In 2015, she spoke about a childhood incident that led to her lifelong fear of water. She stated during a special event for her film Cake, "I basically have a real fear of going underwater. I was a kid and I was riding this tricycle around a swimming pool and I drove my tricycle into the swimming pool and I didn't let go and my brother tried to (help). So, I can't go underwater and no one will believe me. I honestly can't." The incident led to filming a swimming pool scene 30 times on the set of the film with director Daniel Barnz before getting it right.