Derek and Diane Burns are now planning their son's funeral, The Scotsman reported.
They were told in March that a body buried in an unmarked grave might be their son, also named Derek, and last week that the identification was confirmed.
"Right to the end, you still hope. I used to do walks for Missing Persons and you would hear stories of people walking in after 20 years," Burns said. "But as the years pass by, you do start thinking something more serious has happened."
The family filed a missing persons report on Derek in March 1989. They now know that he left their home in West Calder on an apparent whim to visit his girlfriend in West Hampstead, London, and did not take his driver's license, passport or even a change of clothes.
When he got to his girlfriend's, he discovered she no longer wanted the relationship.
Derek's body was not identified because he had no identification, and no one connected a missing man in Scotland with the body in London. An inquest ended with an open verdict.
British Transport Police and the U.K. Missing Persons Bureau have launched Operation Santana, aimed at identifying people who have died on trains or tracks.