As a child he played for the HSV Landau, before moving to his first major youth team, FSV Offenbach. At the age of 15 he moved to Kaiserslautern, for whom he played until 1999. He moved to Karlsruher SC where he played for a year, before going to Borussia Mönchengladbach.
Auer played 23 times for the German under-21 team, scoring 15 goals, and played around 60 times in his youth between the ages of 16 and 20. He helped bring Mainz up to the Bundesliga in 2004.