Of course: How could she explain the “Diary” drawing of 15-year-old Minnie and Monroe, her 35-year-old lover — and her mother’s boyfriend — arguing naked with Monroe’s scrotum in plain view? Or the one of Minnie watching a pimp swagger down San Francisco’s Market Street and wondering, “How does one become a prostitute?”

For the past 27 years, Gloeckner has been one of the premier alternative cartoonists, if not the most prolific. She’s also one of the most explicit: Her first collection of comics and illustrations, 1998′s “A Child’s Life and Other Stories,” was confiscated by British and French customs officials who deemed it pornographic. Their main complaint: a panel of a young Minnie, Hello Kitty diary by her side, about to give a blow job to a much older man.

“Diary of a Teenage Girl,” published late last year, continues the story of Minnie, a precocious and insecure 15-year-old growing up in San Francisco in the late 1970s. Living with a mother who fills the house with her friends and their pot smoke, wine glasses and coke lines, Minnie craves love and attention. Hungry for experience, she begins a tortured affair with the first man who notices her: Monroe, her mother’s boyfriend. Hoping to impress him, and experimenting with her newfound sexual knowledge, Minnie starts to pick up strangers in Golden Gate Park and revels in the lecherous stares of older men. (“I really want to get laid right now,” reads an early entry. “I don’t know if I’ve made that clear — I really love getting fucked.”) After expulsion from various private schools, she runs away to Polk Street, where young gay boys and trannies hang out, and where drugs abound. Eventually, she falls in with Tabatha, a troubled junkie who shoots Minnie up with speed and heroin and prostitutes her for drugs.

In form alone, it’s a groundbreaking work: Minnie’s diary entries intermingle with illustrations; comics move the narrative along. It’s also one of the most brutally honest, shocking, tender and beautiful portrayals of growing up female in America. This diary is no cautionary tale, no “Go Ask Alice.” Minnie is achingly real, and — despite her out-there explorations with drugs and sex — incredibly easy to relate to. She loves Janis Joplin and R. Crumb and science and eggs and the color purple; she spends her allowance on candy; she bullies her little sister.

There’s a reason why Minnie is so realized: like most of Gloeckner’s work, “Diary” is based on her own life.

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In many ways, Gloeckner still seems like a teenager. Her nails are painted black, and she constantly plays with her hair — auburn, long, layered, with bangs. When I arrive at her Long Island home, Avril Lavigne is blasting from her car stereo. When she talks, she sits cross-legged or back on her heels, gesturing wildly, her huge green eyes widening. She looks like a grown-up Minnie.

Gloeckner was born in Philadelphia and moved to San Francisco with her mother, sister and stepfather when she was 11. She and her sister had limited contact with their father, a Philadelphia artist who had a “nomadic life,” Gloeckner says — and a drug problem. “When I was 14, before I’d ever taken any drugs,” she recalls, “he gave me and my sister each this necklace with a little glass vial on it with a top that screwed off. It was filled with cocaine. We were totally puzzled: Why did he give us this? I walked around for months with this thing full of cocaine around my neck.” She laughs. “He was trying to win our favor. And I guess he just imagined that would be a connection to us: We’re teenagers — don’t we like drugs? Well, yeah. But it was kind of premature.”

Although she only saw him once or twice a year, Gloeckner’s father encouraged her drawing ability. At first, she only drew in secret, infuriating her mother by spilling bottles of India ink on her bed. Fascinated by her mother’s copies of Zap - the underground comic that featured R. Crumb, his wife Aline Kominsky and a host of other legendary cartoonists — and inspired by Kominsky’s autobiographical stories, Gloeckner started drawing comics at 15. “It kind of gave me license to do something about my life,” she says of Kominsky’s work, “because it seemed to be autobiographical — although I didn’t know for sure.”

And Gloeckner had a lot of material. Like Minnie, for three years she was secretly involved with her mother’s boyfriend, a 35-year-old real estate salesman who played ball and “palled around” with Gloeckner and her sister. “When he first started showing his interest in me, I was shocked,” says Gloeckner. “I mean, I couldn’t believe it. But I thought, if he’s doing this, it must be OK.

“I was so insecure, and I thought I was so hideously ugly. (I felt) no one would ever want to kiss me or have sex with me, so I’m crazy if I don’t take this opportunity. I just felt lucky.”

At 15, in one of her earliest comics, “Mary the Minor,” Gloeckner began exploring this relationship. “You don’t like me at all. I know you don’t!” Mary cries, tormented by guilt about betraying her mother, but desperately wanting her boyfriend to love her.

“Are you kidding?” he replies. “What dirty old man like me wouldn’t give anything to fuck a 15-year-old regularly?”

San Francisco’s comics community was full of artists using controversial and ultra-personal material, so when Gloeckner began to show her work to local cartoonists — some of whom were casual acquaintances of her mother — most weren’t shocked by its content. It was her talent that caught their attention.

Diane Noomin, creator of “DiDi Glitz” and co-editor of “Twisted Sisters,” an edgy comic by women cartoonists that greatly influenced Gloeckner, recalls a teenaged Gloeckner showing up at her apartment to show her work. “Even then I thought she was way better than many cartoonists who were already in print,” Noomin says.

“I remember thinking, when we looked at her work, nobody would believe they were done by a teenage girl,” says Noomin’s husband, Bill Griffith, creator of “Zippy the Pinhead.” “They were so beyond her years in every way. Phoebe was speaking with a very honest and strangely mature voice.”

Gloeckner continued to publish a few comics a year in small underground comic books like “Weirdo” and “Young Lust.” “You have absolute freedom when you know that very few people will see it,” she says. “There were no limitations as to what you could depict or write about. It was incredibly freeing, and I really enjoyed that.”

But instead of eking out a living as a full-time cartoonist, Gloeckner decided to explore her interest in science at San Francisco State University; she was determined to get an education, unlike her artist-addict father. She received a master’s degree in medical illustration from the University of Texas and began a career drawing pamphlets for doctor’s offices and pharmaceutical companies. Her technical training is immediately evident in Gloeckner’s work, in her intimate knowledge of the human body and in her objective, distant eye. Her illustrations are precise, capturing the most subtle facial expressions. “She’s one of the very best draftsmen in comics, period,” says Griffith. “The drawings are so fully detailed that you can gain as much from a close-up of someone’s face as you can from a page of text.” Noomin agrees: “Due to her medical illustration background she has the ability to depict things so perfectly and true and therefore it’s more shocking to people. You can’t ignore it.”

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In a wooden cabinet at the back of her studio, Gloeckner’s teenage diaries are stored in a giant plastic container. She pulls out a blue folder, worn with age, and shows me the tattered typewritten pages that evoke lines from “Diary.” Aside from the run-on sentences and misspellings, it’s unmistakably Minnie’s story. I catch an actual passage that I recognize from “Diary.” “Lovely lovely colorful daytime. How could you exchange it for a drunken night?”

Gloeckner also wrote in a Hello Kitty diary, which she carried around San Francisco, writing in coffee shops and diners. The first entries are neat, the handwriting large and round and childish, the dates carefully recorded in the small spaces at the top. By the end, during her time with “Tabatha” on the streets of the Tenderloin, the pages are stained with lipstick and blood, the writing haphazard and messy.

But even though “Diary” is based on her own diaries, and even though the book’s cover is a picture of Gloeckner at 15, she hesitates to label it autobiographical, or even semi-autobiographical. She’s been asked this question so many times; answering it obviously frustrates her.

“OK,” she says, taking a deep breath. “I believe that all art is about the artist,” she says. “So, yeah, my work is about me. But being an artist — art is artifice, it’s creation. By reading that book, you’re not experiencing what I experienced. You’re perhaps experiencing my interpretation of it, but you’re bringing yourself to it. In that way, I always hesitate to say this is a true story. I’m not attempting in any way to make documentary. You can never represent everything. It’s always a selective process.

“I mean, really, my motivation is, ‘This all happened to me. I feel really totally fucked-up. I don’t understand any of this. Let’s look at it. Let’s not look at it sideways or make it look prettier, but let’s just look at it for what it is.’ I think the reason people relate to it is because I don’t avoid things that may seem unpleasant. I don’t really judge things … I just look at them.”

“Diary” is different, somewhat, from Gloeckner’s actual adolescence: She omitted unnecessary characters, merged characters, and crafted an ending. But even though she refers to Minnie as a character, the two are so intertwined that Gloeckner moves seamlessly between referring to herself and referring to Minnie.

“As I grew older, I had experiences that made me feel that perhaps Minnie didn’t have such a great upbringing,” she says. “It’s possible to develop a compassion for yourself … it’s almost this schizophrenic thing, where you can look at yourself and think, ‘Gee, that poor girl, I wish I could help her.’

“In everyday life I tend to hate myself half the time, but yet, I love that poor little girl, and look at all those assholes — I’ve really got to help her! And by extension, I understand all those other little girls that this might be happening to, or who might be having these disturbing feelings, and I love them all and I’d love to give them a voice. She’s not me anymore. She’s Minnie. She’s all these girls … She doesn’t have to be me. She’s bigger than me.”

Talking to Gloeckner about Minnie does feel slightly schizophrenic: I’m constantly aware that I have to choose when asking questions. Am I asking about Minnie, or Gloeckner?

On our way to lunch at a Mexican restaurant in her neighborhood, Gloeckner needed to drop off a package at the post office. “I’m going to smoke a cigarette while I wait,” I told her when we pulled into the parking lot.

“I love to smoke,” she said wistfully. “I smoked two packs a day until my kids were born.”

“But Minnie doesn’t smoke,” I pointed out.

“Oh,” says Gloeckner, “Minnie didn’t start until she was 19.”

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Gloeckner has always toyed with the idea of using her teenage diaries as the basis for a book, but it wasn’t until a few years ago, after she’d been happily married to her third husband (a chemistry professor at SUNY-Stony Brook), and had children, that she decided to try. “If I had written this book when I was 20, I would’ve been so judgmental,” she says. “I would’ve written it almost in a punishing manner, and not giving this voice any freedom to emerge. I would’ve been ashamed and horrified. If I wrote it when I was 30, I would’ve been too upset. I had my first child; I would’ve written it in a reactionary mode. It wasn’t until now, that I can write with a calmer eye, and I can just let it come out the way it did.”

But behind her Zen approach lies a mountain of residual anger: anger at her mother, at her mother’s boyfriend, and, especially, at a culture that simultaneously hyper-sexualizes teenage girls while projecting standards of innocence upon them.

“Just looking at [the diaries], I got incredibly pissed,” she says. “Sometimes when I would tell people that the first person I had sex with was my mom’s boyfriend, they would romanticize that. Some man said to me, ‘Well, weren’t you lucky that you had an older man who could introduce you …’ It’s like a romantic fantasy. And it’s insane. Even women would say things like that. So I guess it really pisses me off — the fantasies built around that particular kind of relationship.

“When I looked around, before I did that book, all I could see was projection and fantasy on teenage girls — which just infuriated me. And at the same time I’m thinking, how can this man, who’s my mother’s boyfriend, want to have sex with me? There’s something perverse about having sex with a woman and her daughter. It’s like incest, whether or not you’re related to those people by blood. It’s breaking a family. The mother and the daughter become rivals. The mother is no longer protecting the daughter. In that way, it’s incredibly destructive. In my situation it’s harder to see, perhaps, because the family was never really together — but it destroys all possibility of that family ever healing and coming together. There’s a rift created by this man who’s decided to do that.” Gloeckner’s mother eventually found out about her relationship with her boyfriend — a friend whom Gloeckner had entrusted with the secret told her — and she drunkenly confronted him at a bar. “How many times did you pork her, Monroe?” Minnie’s mother says in “Diary.” “How many? Was it good?”

“Instead of getting angry at him, she became angry at me,” Gloeckner says of her mother’s reaction. “There was no ‘protect my child’ impulse kindled. I’ve always thought that she’s never taken any responsibility for that situation. It hurt it a lot. I suddenly realized that my mother was not someone I could trust and rely on. At that age, I still was able to dream that she would come to my rescue.” (Her mother is, amazingly, still friends with the man.)

Gloeckner’s mother has read “A Child’s Life,” she says, but hasn’t read “Diary.” “She said it was too upsetting,” says Gloeckner. “In one way she’s proud of me; in another way she’s furious. She tends to be sarcastic when she talks to me; she always has been. Like, I’m teaching (a drawing class) and she said, ‘Oh, well, are you going to teach them all to take their diaries and make a book out of it?’”

“What Phoebe has managed to do is make art out of harrowing experiences,” says Noomin. “And they’re not just vomited onto the page. It’s not just ‘Well, this terrible thing happened, and I did a comic about it, and everyone should be interested because it’s about child abuse.’ It’s way beyond that. She’s a very evocative writer. She’s very powerful.”

Gloeckner’s work especially resonates with girls and women who have experienced sexual abuse, says Richard Grossinger, co-publisher of Frog, Ltd./North Atlantic Books, her publisher. “I don’t think they’re comforting stories,” he says. “But the comfort lies in having the stories told at all.”

Despite Gloeckner’s status among other cartoonists (“Diary” blew me away. It had to be the most outstanding book of last year,” says legendary cartoonist Kim Deitch), her work, like many alternative cartoonists’, hasn’t sold exceptionally well — partly because of the explicit sexual images. “Her work should do far better than it does,” says Grossinger. “It suffers somewhat, especially the first book, from bookstores not wanting to carry it. They’re worried some kid is going to take it home and the parents are going to make a fuss.”

Gloeckner seems unaware, to a certain extent, of the shocking nature of her work. Probably because her drawings depicting teen sexuality (one involves Minnie and her best friend Kimmie sitting naked on Monroe’s bed after a threesome) aren’t meant to court controversy. “I guess I don’t really see it,” she says. “I kind of live in this bubble of seclusion in the garage in suburbia, and even when I lived in San Francisco, I lived in the bubble of underground cartoonists, where nothing was shocking. Although I know there’s this big dangerous world out there that thinks what I do is shocking or weird, if I internalized that and looked at myself that way — I couldn’t look. I try not to think too much about other people’s view.”

“I don’t think she wants to push boundaries,” says Noomin. “She’s just doing stuff from very deep inside and she won’t hold back. She has integrity and honesty; she won’t compromise. If it involves drawing something that somebody’s going to interpret as pornographic, so be it.”

In “A Child’s Life,” a comic called “Fun Things to Do With Little Girls” is signed “Phoebe ‘Never Gets Over Anything’ Gloeckner.”

“I was making fun of myself,” she says. “I hadn’t said everything I wanted to say, (and) I could see very clearly that anyone looking at it might think, ‘Jesus Christ, she’s writing another thing about this?’ And I knew I would do it again, too.”

But with “Diary,” Gloeckner says she’s finished with that period of her life. She wants to write another book, and, possibly, make a movie. What would Minnie think of her life now? I ask.

“I don’t think she would understand how to get from where she is then to where I am now,” Gloeckner says. “But I think that’s kind of what she wants. She just wants to be a creator. She has that energy. She wants to be an artist. I don’t think she’d be surprised. But living in Long Island, I don’t know …” She laughs. “She might be very disappointed.”