Sources close to the couple say that it was a "natural childbirth" and that they have not yet decided on the boy's name. Beatie's wife, Nancy, will be breastfeeding their son, as she did with their daughter, Susan Juliette, who was born last June.
Photos of a bearded Beatie with a pregnant belly caused a sensation last year, leading to headlines about the world's first "pregnant man."
Born a woman named Tracy, Thomas Beatie, now 35, had sex-reassignment surgery and legally changed his gender from female to male in Hawaii.
Beatie, who kept his female reproductive organs, says that he decided to bear children, when his wife Nancy, 46, was not able to.
The couple described their unusual path to parenthood in an exclusive interview with Barbara Walters last year, during which they revealed that Thomas was expecting a second child.
Then in his first trimester, Beatie told Walters he did not go back on the male hormone testosterone after Susan's birth so he could have another baby.
"I feel good," he said. "I had my checkups with my hormone level, as far as the HCG. And everything is right on track."
In last year's exclusive interview, Beatie spoke to Walters about Susan's birth, which was also not via Caesarean section. He was in labor for 40 hours; Nancy Beatie cut the umbilical cord.
Last spring, Thomas Beatie wrote an article in the national gay magazine The Advocate, revealing that he was legally male and that he was pregnant. He released a photo showing his bearded face and pregnant belly. The news -- and the controversial photo -- ignited a media frenzy and provoked questions about traditional notions about sex and gender.
"Hiding a pregnant man is like hiding an 800-pound gorilla," he said of his decision to go public. "Nancy and I wanted to tell our story from our own mouths before it got out."
Beatie says he was surprised at how quickly the news of the "pregnant man" spread.
"I was shocked that it looped around the world in 24 hours," he told Walters. "I mean, it was on Chinese Web sites and, you know, Web sites in Romania and Russia and Brazil."
He became an instant target of the tabloids and paparazzi, and fodder for talk shows and late-night television. Some people called Beatie a freak. He received death threats, and thousands of hateful comments still litter the Internet. To this day, he continues to receive anonymous hate messages.
For months after Susan's birth, Thomas Beatie, 35, and his wife, Nancy Beatie, 46, lived a quiet life in Bend, Ore., where they own a tee shirt company called Define Normal.
Despite concerns for his family's safety, Thomas Beatie said he won't let fear rule their lives and he feels they are a traditional family.
"We are a man, woman and child. It's ironic that we are so different but yet, we're just a family, just the same as anyone else," he said.
When asked why he makes many people uneasy, Beatie said, "I think that people are not used to seeing the image of a pregnant man. And it's causing a lot of people to think. … I used my female reproductive organs to become a father."
Thomas Beatie was born Tracy and grew up in Hawaii. A beautiful young girl, Beatie said he never felt particularly feminine growing up.
"I felt rough and tumbly," he said. "I didn't like frilly stuff."
In 1986, when Beatie was 12 years old, his mother committed suicide. He said his father pushed his tomboy daughter into becoming a model.
"Back then, I did not see an attractive young girl," he said. "Putting on makeup, I felt like I was putting on a costume."
At 14, he entered the Miss Teen Hawaii USA contest and became a finalist.
"I remember feeling uncomfortable on stage," he said.
Eventually, Beatie traded modeling and pageants for karate and the gym and began to dress like a man and use the men's bathroom. Although he had several boyfriends, he now says he hated sex.
At 24, Beatie began a lesbian relationship with Nancy, a bodybuilder, and moved in with her and her two daughters from a previous marriage.
In 1998, he decided to change genders. Psychological testing confirmed that he identified with being a male and he began to medically transform his body, first, by injecting the male hormone testosterone.
"My voice started to change," he said. "It started to crack like I was going through puberty. My bones felt stronger, my ligaments felt stronger. I started to grow facial hair."
In 2002, Thomas Beatie, still legally Tracy, had sex reassignment surgery to remove his breasts.
"That day was -- the most liberating day of my life," he said. "I literally felt like a weight was lifted from my chest."
To legally change genders is a long and complicated process. No federal law applies and state requirements vary.
In Hawaii, with a letter from a doctor certifying Beatie's psychological testing and irreversible surgery, he was legally allowed to change his birth certificate from female to male and his name from Tracy to Thomas.
Though Beatie physically and legally transformed himself from a woman to a man, he did not have "bottom" surgery, known as phalloplasty, to create an artificial penis. He also left his female reproductive organs in place.
"I don't feel like removing your sexual reproductive organs will make you any more of a man or any less of a woman," he said.
Last year on "20/20," Walters reported on how children as young as 5 years old are transitioning from one gender to another. And in the last few years transgender people have gained gradual acceptance, even showing up in Hollywood plot lines, such as on the TV series "Ugly Betty" and "Dirty Sexy Money."
But what happens when that transgender child grows up and wants to have a baby?
In 2003, Thomas and Nancy Beatie were legally married, and like many couples, they decided to start a family. The couple wanted to have a biological link to their child, but Nancy Beatie had a hysterectomy.
The couple did not want to hire a surrogate to carry Thomas Beatie's harvested eggs, feeling no surrogate could be as conscientious as he would be.
So how does a man who was once a woman get pregnant? The first step was to stop taking testosterone, his male hormone. After four months he began menstruating.
The Beaties then needed a doctor who could help them obtain donor sperm and inseminate it into Thomas Beatie, but nine doctors rejected them.
In the end, the Beaties did it all themselves. First, they bought donor sperm on the Internet and Nancy Beatie used a syringe she had bought at a pet store to inseminate her husband. Soon after, a home pregnancy test confirmed that he was pregnant.
Thomas Beatie said that pregnancy did not make him feel more like a woman.
"I did not feel maternal or motherly or womanly and pregnant," he said. "I felt like Nancy's husband, and I felt like the father of my child."
The Beaties said they were surprised that some gay, lesbian and transgender groups did not support them. Before his appearance on Oprah Winfrey's talk show in the spring, Thomas Beatie said representatives from several gay and transgender groups warned him not to do it.
"There are six different organizations on the phone doing a conference call with us saying, 'you can't go public. You can't talk about this. You need to hide. You need to be embarrassed,'" he said.
But the Beaties received support from hundreds of individuals.
"We got letters and gifts from all around the world, from gays, lesbians, mainstream America and beyond," Thomas Beatie said.
They also received acceptance among their Oregon neighbors, who threw a baby shower for Thomas Beatie a few weeks before his due date.
While Thomas Beatie's body went through changes, so did his wife's. She said, "My breasts started lactating."
She has been breast-feeding Susan for four months.
Thomas Beatie said he and his wife are clear on their parental roles.
"I am my daughter's father, and that's all I'll ever be to her," he said. "Nancy is Susan's mother."
But state officials in Oregon had a different view when it came to the baby's birth certificate.
"The nurse in charge of birth certificates came in and said, 'Portland won't allow this. That means, Thomas, we're going to put you as mother and Nancy as father,'" he said.
According to Oregon law, the person who gives birth is normally listed as mother. But when Thomas and Nancy Beatie complained, the certificate was changed again.
"The woman down at Vital Statistics in Portland decided to change it to say Parent/Parent, which is for same-sex couples in a domestic partnership," Thomas Beatie said.
The Beaties insisted that they are a married, heterosexual couple and that the birth certificate should list them as father and mother.
Legal experts say that regardless of how Thomas Beatie is listed, his parental rights are protected because he is the baby's biological parent. But because she has no biological tie, Nancy Beatie could find her rights threatened.
In order to secure Nancy Beatie's parental rights, legal experts say the Beaties need to do what many same-sex couples with children do and have Nancy Beatie, the nonbiological parent, adopt Susan.
Instead they want to fight to change the birth certificate. They asked the American Civil Liberties Union to take their case but were turned down. They are still seeking legal representation.
"I feel that it's a flawed document," Thomas Beatie said. "We'd like to see this process remedied for the next child, for the next pregnant man."
Life in the Beatie home is pretty typical. Thomas Beatie tends the garden, Nancy Beatie breast-feeds the baby. But while the Beaties paint a picture of themselves as a normal, everyday family, others see them as outsiders and question their claims and motivations. Many have accused the Beaties of going public to profit from their story.
In fact, the Beaties have made some money. They sold photographs of their family to Getty Images, a photo agency, and were paid to appear in a British documentary that aired on the Discovery Health Channel.
Thomas Beatie has also written a book about his life, "Labor of Love," but he claimed that money has never been their motivation.
"We've turned down about $2 million altogether from people wanting to do all sorts of things with us," Beatie said. "But as far as, you know, doing it for the fame, I have to say I'm infamous. I mean, who wants to be unpopular, controversial and despised?"
But the notoriety has not stopped them from adding to their family. Nancy Beatie inseminated him again.
The Beaties are already telling Susan about the unusual circumstances of her birth. Thomas Beatie said he reads his daughter, whom he calls "Sweetpea," the Eric Carle book "Mr. Seahorse," a children's picture book that shows how male sea horses carry their offspring.
"And I point to the picture at the end of the book where Mr. Seahorse has his babies and say, 'This is what I did with you, Sweetpea, and you're just that one special sea horse,'" he said.
"I just wish that people could be more tolerant to different types of families," Nancy Beatie said. "And I want them to know that we love each other, and we're going to love this baby."