Janzen played baseball at Gainesville High School in Gainesville, Florida but did not plan to play baseball after high school and was considering, instead, pursuing a career as a professional bowler. However, after graduating, Janzen spent a summer playing American Legion Baseball with coach Kevin Maris, the son of Roger Maris, and added 10 mph (16 km/h) to his fastball. He signed with the New York Yankees as an amateur free agent on August 8, 1991.
Janzen was assigned to the Gulf Coast League to start his professional career. By 1994, he had reached the South Atlantic League with the Greensboro Bats and was described in the Greensboro News & Record as one of the "Yankees' prized pitching prospects."
During the 1995 season, Janzen was considered one of the best prospects in the Yankees' system and was the centerpiece of a trade deadline deal to the Toronto Blue Jays for reigning American League Cy Young Award winner David Cone. The trade has been retrospectively regarded one of the most lopsided trade deadline swaps in league history.

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