Elian was last seen playing in Lively Park in Irving, Texas at approximately 6:30 p.m. on June 21, 2006. He was with his four-year-old brother, Alexis, at the time. Authorities initially believed the child had simply become lost, but they reconsidered this theory after an extensive search of the area turned up no signs of him.

Elian was being watched by his mother, Yancy Majano, and an adult male acquaintance at the time of his disappearance. Alexis was taken from his mother's custody and put in a foster home the day after his brother's disappearance, as Child Protective Services was concerned that the children had not been properly supervised. Yancy allegedly made conflicting statements about the events leading up to Elian's disappearance. She says she took her eyes off her sons for less than a minute, but investigators believe the children were unsupervised for up to eight minutes. Alexis is now in the custody of an older half-brother. Yancy visits him on weekends.

People searching for Elian discovered a sinkhole about 100 feet from the Lively Park parking lot. The sinkhole, which is was twelve to eighteen feet deep and eighteen inches in diameter, was caused by a broken underground sewer pipe. Dogs tracked Elian's scent to the sinkhole, and Alexis pointed to it and told investigators, "Elian fell." The city began repairing the sewer pipe immediately, and a nearby water treatment plant began monitoring its flows looking for the child's remains. No evidence was located, however. Authorities searched the sewer system with cameras and found no trace of Elian; they are almost certain he is not in the sewer pipes.

Investigators believe Elian could have been abducted, but given that it was broad daylight and the park was full of people, it is unlikely that an abductor could have gotten away with the child without being seen. Little evidence is available regarding Elian's disappearance. His case remains unsolved.