"This is how I was born. I mean, there's no doubt in my mind," Chaz told "Nightline" anchor Cynthia McFadden.
In a rare and candid interview at his home in West Hollywood, Calif., Bono, 42, openly talked about going under the knife and going through a process known as "transitioning" -- changing physically from female to male. This life-altering decision is described in his latest memoir, "Transition: The Story of How I Became a Man," and in his documentary, "Becoming Chaz."
"It's actually pretty simple if you look at it," Bono said. "We all in the womb start out as female and then hormones come and we either stay female or we become male. I think of it as hormones that, you know, went in the brain but not in the body, and that's all being transgender is. It's just that the sex of your body and the gender of the brain don't match up."
It took Bono nearly four decades to reach the point at which he decided he wanted to have gender reassignment surgery to become a male. The process began after Bono's 40th birthday in March 2009 -- over a decade after he had publically come out as a lesbian.
Bono began receiving testosterone injections, which helped make his voice deeper and produced facial hair. He also had his breasts surgically removed.
"If you are a man and you have breasts, any man would want to have them removed," Bono said. "It is scary for a woman to think about it because it is something that they are really attached to. Being male and having breasts is about the worst thing I could imagine."
But the process also had an incredible emotional toll attached to it, not just for Bono, but also for his family, including his mother, Cher, and his partner, Jennifer Elia.
"If I was average Joe I would have done this years ago," Bono said. "I felt a tremendous responsibility not just for myself, but what am I doing to my family? What am I going to put them through?"
In an exclusive interview with "Nightline" anchor Cynthia McFadden last year, Cher talked about how difficult it was for her when her daughter first came out as a lesbian, and then told her she wanted to become a man.
Elia, Bono's fiancée, said she was also very nervous about her partner having the surgery and how the public would react to his new transformation afterwards.
"I was terrified primarily of what other people would say and think," Elia told McFadden. "I thought people were going to throw dog feces at our door."
Bono shared his partner's sentiment: "I was worried about being followed by the tabloids again. I risked a lot but I finally got to the place where I knew this is what I'm supposed to do."
Elia and Bono met in 2005 and hit it off immediately. Just a few months into their relationship, Elia heard the bombshell. Chaz was thinking of changing his gender, and then he decided to go ahead with it.
"I was like, 'You're going to go do this, OK, what about me? What about everyone in your life? We're just supposed to adjust?'" Elia said. "I didn't go through it sober."
Both of them suffered from substance abuse -- Bono to pain killers and Elia to alcohol -- but Elia decided to stay with her partner as he began taking testosterone and their relationship was severely tested.
"Hormones change people and I think he's leveled out right now," she said. "There was a period where I felt they were kind of spiked. The testosterone was like really machismo, and it was hard to deal with."
Elia added that she had a rough time living through and seeing Bono change from Chastity to Chaz.
"There is a softness that is gone for sure," she said. "Literally at that point when I was watching the female essence leave his body, it was hard."
But an added benefit of the hormone injections, the couple said, is that the testosterone has improved their sex life.
"[It's] just a higher sex drive, like all men," Bono said. "It is different."
"It's more intimate. It's more personal," Elia said. "And it's more frequent."
It was after Bono underwent surgery to have his breasts removed that Elia said she had a realization about the person Chaz wanted to be.
"I was terrified to see what the results were going to look like," she said. "When it did happen and I saw the reveal, I had a relief go through me. I was like, 'Oh, so this is how you're supposed to look. OK, now it all makes sense.'"
Ecstatic about having the surgery, Bono said he hated his breasts from the moment they developed and that he has felt much better since having them removed.
"I never wear a shirt at home anymore, ever," he said.
Anatomically, Bono remains a woman from the waist down and said he doesn't have any plans to undergo corrective surgery yet because that type of surgery is still risky.
"I'm just kind of waiting to see what happens and hoping that there are medical advances made and it gets a little better because right now the risk-reward ratio is just not quite right," he said. "The majority of [transgender people] don't have bottom surgery because of that."
But even without physically having a penis, Bono said he has always felt like a man, long before taking hormone injections.
"That's not to say I wouldn't like a penis," he said. "I really would like one and I hope that someday I will get one."
His partner also said she completely views Bono now as a male. "I don't even think of him at all as a woman. I haven't for years," Elia said.
Since the transition, Bono said he's the same person he's always been, but just in a different body.
"I am the male version of my former self," he said.
In an exclusive interview with "Nightline" anchor Cynthia McFadden last year, Cher talked about some of the concerns that she had about Chaz transitioning.
"I was really frightened in the beginning, and also, I felt that the doctors did not do their due diligence," Cher said at the time, adding that she also supported Chaz and his decision.
"I have two sons," Cher said in the interview. "Never thought that would be, but, you know, you go through life and you get what you get."
Bono said that his relationship with his mother continues to "move in the right direction."
Bono was first introduced to the public on his parents' popular '70s television series, "The Sonny & Cher Comedy Hour." Often seen wearing frilly dresses and shiny shoes on the show, Bono said that even when he was a little girl, he was friends with and liked to dress like boys.
"My seventh and eighth grade year was a particularly hellacious year for me," he said. "Puberty. And I was at a school that just wasn't appropriate for my needs. It was just very straight, strict academic school."
Sonny Bono and Cher divorced in 1975 when Bono was 4. He wrote in his book, "Transition," that he could dress and act like a boy at his father's house, but at his mother's house, it wasn't so easy.
"I grew up in the '70s and '80s," he said. "We didn't know anything about this and my mom has her first child who's a girl and, you know, had the kind of expectations that any mother would have of their first-born daughter...she said things like, 'You look like a truck driver, you look like a slob'...I just dealt with it."
Bono also remembers when he first started to think he was a lesbian.
"It was my 13th birthday, actually, and my best friend, we were living in New York, my mom was doing a play there," Bono said. "I mistook sexual orientation for gender identity. I went for the obvious answer."
Although he was outed at 18 by a tabloid magazine in 1987, Bono didn't come out publically as a lesbian until 1995. Even though he had serious, long-term relationships with women at the time, he said something did not feel right.
"I just thought that something was wrong with me," Bono said. "Like I am not being a good lesbian...because I was really a man so I never wanted to be a woman. That's how I was failing as a lesbian."
Now, after being reintroduced to the world as Chaz, Bono said he had a newfound sense of peace.
"I risked a lot but I finally got to the place where I knew this is what I'm supposed to do," he said. "I had absolute faith in no matter what, even if it was rocky or difficult, everything in the end was going to be fine, and it was. It has exceeded every expectation that I've had."