The Minnesota Twins signed Hendriks as a non-drafted free agent on February 25, 2007, as he was signed by scout Howard Norsetter. He began his professional career in the Gulf Coast League, leading the GCL Twins in strikeouts with 52. In 44 innings of work, Hendriks went 4-2, posting a 2.05 earned run average. He made ten starts, walked only 11, and held the opposition to a .237 batting average.
A nerve injury robbed Hendriks of his 2008 season, as he did not appear in a single game. He would begin the 2009 season with Elizabethton, but after dominating in three starts, he was promoted to Beloit, where he would start 11 games.
In those 11 games, Hendriks went 3-5, but was solid throughout. The Aussie struck out nearly a batter per inning, and was a cog in the rotation after being promoted on July 8. In 66.2 innings, Hendriks walked only 15, and showed pinpoint control all season long.
This season he has been on another level, and finished the first month of the season with the best earned run average in the system. In four starts, Hendriks went 1-0, and posted a 0.41 ERA. In 22 innings, Hendriks was second in the system with 26 strikeouts, and walked only two. He allowed only one earned run all month long, and let up only seven hits. Opponents batted only .096 against him.