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Travolta was in a relationship with actress Diana Hyland, whom he met while filming The Boy in the Plastic Bubble; Hyland died of breast cancer in 1977.

Travolta has been married to actress Kelly Preston since 1991. Travolta married actress Kelly Preston in 1991. The couple had a son, Jett (1992–2009). Their daughter, Ella Bleu, was born in 2000. On May 18, 2010, Travolta and Preston announced that she was pregnant with the couple's third child, later confirmed to be a boy. Their son, Benjamin, was born on November 23, 2010 in Florida.

Travolta and Preston have regularly attended marriage counseling; Travolta has stated that therapy has helped the marriage.

Travolta is a certified private pilot and owns five aircraft, including an ex-Qantas Boeing 707–138 airliner. The plane bears the name Jett Clipper Ella in honor of his children. Pan American World Airwayswas a large operator of the Boeing 707 and used Clipper in its names. The 707 aircraft bears the marks of Qantas, as Travolta acts as an official goodwill ambassador for the airline wherever he flies. His $4.9 million estate in the Jumbolair subdivision in Ocala, Florida, is situated on Greystone Airport with its own runway and taxiway right to his front door. On September 13, 2010, during the first episode of the final season of her talk showOprah Winfrey announced that she would be taking her entire studio audience on an 8-day expenses-paid trip to Australia, with Travolta serving as pilot for the trip. He had helped Winfrey plan the trip for over a year. On 24 Nov. 1992 Travolta piloting his Gulfstream N728T at night (on top of a solid undercast) had a total electrical system failure while flying IFR into DCA. During the emergency landing there was a near mid-air collision with USAir Boeing 727, due to a risky decision by an air trafic controller.

Travolta has been a practitioner of Scientology since 1975 when he was given the book Dianetics while filming the movie The Devil's Rain in Durango, Mexico. After the 2010 Haiti earthquake, joining other celebrities in helping with the relief efforts, Travolta flew his 707 full of supplies, doctors, and Scientologist Volunteer Ministers into the disaster area.

In June 2010, Travolta and Preston donated $10,000 to the Nelson Mandela Children's Fund while on a trip to South Africa.

Son's death On January 2, 2009, Travolta and Preston's son, Jett, died while on their holiday vacation in The Bahamas. A Bahamian death certificate was issued, attributing the cause of death to a seizure. Jett, who had a history of seizures, reportedly suffered from Kawasaki disease as an infant. On September 24, 2009, long a source of speculation, Travolta and Preston confirmed that their son had autism and suffered regular seizures. They made their statements while giving a testimony after a multi-million dollar extortion plot against them regarding the circumstances of their son's death. After a mistrial, Travolta dropped the charges. Travolta has credited his family and faith in helping him survive the tragic death of his son, and in moving forward with his film career