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Gloeckner was born in Philadelphia, Pennsylvania. Her mother was a librarian and her father, David Gloeckner, was a commercial illustrator. Her father's family was Quaker and she attended Quaker schools when she was young. She has a younger sister.
Gloeckner's parents divorced when she was 4 years old. In 1972, when she was 11 or 12 years old, her mother remarried and the family moved to San Francisco. She attended several Bay Area schools, including The Urban School of San Francisco and Lick-Wilmerding High School. She was a boarding student at Castilleja (in Palo Alto) for a year, but returned to San Francisco to live with her mother, her mother's boyfriend, and her sister, when she was 14.
Gloeckner became interested in medical illustration through her maternal grandfather, an antique dealer who collected and sold old books, and her paternal grandmother, Dr. Louise Carpenter Gloeckner, who was a physician in Philadelphia and was the first woman to be elected vice president of the American Medical Association.
Gloeckner worked prolifically as a medical illustrator since 1988, and her training is evident in her paintings and comics art, which are highly detailed and often prominently feature the human body. Her first prominent work in fiction publishing, a series of illustrations for the RE/Search edition of J. G. Ballard's novel The Atrocity Exhibition, used clinical images of internal anatomy, sex, and physical trauma in ambiguous and evocative combinations.
Her early comics work, in the form of short stories published in a variety of underground anthologies including Wimmen's Comix, Weirdo, Young Lust, and Twisted Sisters, and in the tabloid zine, RE/Search (numbered volumes), was sporadic and rarely seen until the 1998 release of the collection A Child's Life and Other Stories. This was followed by her 2002 graphic novel The Diary of a Teenage Girl: An Account in Words and Pictures, which revisited the troubled life of the young character (usually referred to as "Minnie Goetze") previously featured in some of her comics, this time in an unusual combination of prose, illustration, and short comics scenes.
Her novel and many of her short stories are semi-autobiographical, a frequent cause of comment due to their depiction of sex, drug use, and childhood traumas; however, Gloeckner has stated that she regards them as fiction. Sexual content led to A Child's Life and Other Stories being banned from the public library in Stockton, California, after it was checked out by an 11-year-old reader. The mayor of Stockton called the book "a how-to book for pedophiles." The graphic novel was also classified as pornography and refused entry by customs officials in both France and England.
Less controversial, and actually intended for children, is the book Weird Things You Can Grow, published by Random House, and books in the series beginning with Tales Too Funny to be True published by HarperCollins, for which she did the illustrations.
2008: Guggenheim fellowship working on research for a graphic novel about families living in Ciudad Juárez; project inspired by experiences in Ciudad Juarez while researching her story in the 2008 book, I Live Here
Kirshner, Mia, Mike Simons, and Paul Shoebridge. "I Live Here." NY: Pantheon Graphic Novels, 2008. ISBN978-0375424786
Gloeckner, Phoebe. "Autobiography: The Process Negates the Term." Chaney, Michael A. Graphic Subjects: Critical Essays on Autobiography and Graphic Novels. Madison, Wisconsin: The University of Wisconsin Press, 2011. ISBN978-0-299-25104-8OCLC665064402
Pekar, Harvey, and Phoebe Gloeckner. Graphic Novels A Conversation : a Panel Discussion with Harvey Pekar and Phoebe Gloeckner. University Park, Pa: Pennsylvania State University, 2007. Recorded on February 22, 2007, at the Foster Auditorium, Pattee Library and Paterno Library, Penn State University. OCLC368266902
Lealess, Jacqueline. Making a Spectacle The Comics of Debbie Drechsler, Phoebe Gloeckner, Diane DiMassa, and Julie Doucet. Ottawa: Library and Archives Canada = Bibliothèque et Archives Canada, 2007. Thesis/dissertation. ISBN978-0-494-15688-9OCLC233786256