Heche's relationship with comedian Ellen DeGeneres and the events following their breakup became subjects of widespread media interest. The couple started dating in 1997 shortly after the famous "Puppy Episode" of DeGeneres' eponymous sitcom. At one point, the two said they would get a civil union if such became legal in Vermont. They also worked on film and TV projects together. The couple split up in August 2000 and Heche began dating cameraman Coleman Laffoon, whom she met while Laffoon was filming a comedy special for DeGeneres. They were married in September 2001 and have a son, Homer Heche Laffoon (born on March 2, 2002). On January 24, 2007, it was confirmed that Heche had split from Laffoon after five years of marriage. Lafoon filed for divorce on February 2, 2007. Sources say Heche left him for Men in Trees co-star James Tupper. Heche's rep had no comment, but the actress herself confirmed the relationship in October 2007 while appearing on Late Show with David Letterman.
A year after her split with DeGeneres, Heche made claims in television interviews and in her autobiography, Call Me Crazy, that she was mentally ill for the first 31 years of her life after being sexually abused by her father. She also claimed to have an alter ego that was the daughter of God and half-sibling of Jesus named "Celestia," who had contacts with extraterrestrial life forms. In her book, she explained that before her split with DeGeneres, she was contacted by God and told he would walk with her for seven days.
Her mother, Dr. Nancy Heche, is a professional Christian psychotherapist. She has toured the USA as a Christian speaker giving testimony of the impact on her life by her husband's death from AIDS in 1983, by the sudden "death bed" revelation of his secret adulterous relationship, and by Anne's lesbian relationship. Nancy Heche has described how her spiritual views toward homosexuals have changed. In her recent book, The Truth Comes Out she describes how prayers and her own personal spiritual awakening coincided with Anne's change from a lesbian relationship.
Heche said her split with DeGeneres was not because of a change in her own sexual orientation. In an interview with The Advocate following the split, Heche said she does not give a label to her own sexual orientation and said "I have been very clear to everybody that just because I'm getting married does not mean I call myself a straight."
Before dating DeGeneres, Heche dated comedian Steve Martin for two years (she is rumored to be the basis for Heather Graham's character in Bowfinger, although Martin denies it). She also dated musician Lindsey Buckingham of Fleetwood Mac for a year in the early 1990s. Some speculate that she is the subject of Buckingham's barbed song "Come." Others speculate that he wrote "Down on Rodeo" (on the Under the Skin album) about her because he can be heard saying "Do you hear me, Annie?" at the end.
In 1994, Heche's sister, Susan Bergman, wrote a book about the family and their relationship with their father titled Anonymity. Heche and Bergman were reportedly estranged after the release of Bergman's book; Bergman died in January 2006.