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Rudolph was born in Gainesville, Florida, the daughter of the late soul singer Minnie Riperton (also known as Andrea Davis) and composer, songwriter and producer Richard Rudolph.[1] Her father was Jewish and her mother African American.[2] She was in the studio with her mother on the day Riperton recorded "Lovin' You"; one can hear her mother sing "Maya, Maya, Maya" to her near the end of the track. Riperton passed away at age 31, from cancer, short of her daughter's seventh birthday. This loss at a young age and growing up multiracial had an effect, according to a July 2001 Rosie magazine article: "My mom was black and my dad is Jewish, and I lost my mom when I was seven. That made me feel really different from other kids."

Growing up, Maya attended St. Augustine by the Sea School, where she met childhood friend Gwyneth Paltrow. The Paltrows and the Rudolphs became family friends. She attended high school in Santa Monica, California, and continued her education at the University of California, Santa Cruz, where she graduated in 1995 with a B.A. in photography from Porter College.

Rudolph and filmmaker Paul Thomas Anderson are in a relationship, and have a daughter, Pearl Bailey Anderson, born on October 15, 2005.