A baseball scout discovered Langdon playing catch with his father in the parking lot of their hotel during Langdon's recruiting trip to Duke and was immediately impressed. Langdon was selected in the 6th round of the 1994 Major League Baseball draft out of high school by the San Diego Padres, ahead of such eventual All-Stars as Carl Pavano and Plácido Polanco. At the time he was the highest drafted player ever out of Alaska. He signed with the Padres and received a $230,000 signing bonus. Because NCAA rules at the time prevented a player from receiving a scholarship in one sport while playing another professionally, Langdon had to play basketball at Duke without a scholarship while playing Minor League Baseball during the summer. In three seasons in the minors, he played in 50 games for the Spokane Indians and Idaho Falls Braves.
