The 52-year-old Mills has been Terry Francona's bench coach in Boston for the past six seasons. He'll manage in the majors for the first time, though he's managed a total of 11 seasons in the minors, with affiliates for the Chicago Cubs (1987-92), Colorado Rockies (1993-96) and Los Angeles Dodgers (2002).
The Astros fired Cecil Cooper on Sept 21. Third-base coach Dave Clark served as interim manager for the final 13 games and Houston finished 74-88. Clark was one of 10 candidates to interview for the full-time position, and he spoke for a third time with the team on Tuesday.
The Astros made an offer to former Nationals manager Manny Acta over the weekend, but Acta accepted the Cleveland Indians' offer instead.
Mills will have work to do. The Astros have endured two losing seasons in the four years since reaching the World Series in 2005, and Mills is the fourth manager hired since the middle of the 2004 season.
Houston was 49-46 on July 22, one game out of first place in the NL Central, then lost 42 of their last 67 games as the starting pitching deteriorated.
Pitcher Roy Oswalt's season was cut short by back problems and he'll spend the offseason working to recover in time for spring training. The Astros' ace won a career-low eight games in 30 starts, finished with a career-high 4.12 ERA and set a team record with 16 no-decisions.
Houston also signed free agents Mike Hampton and Russ Ortiz to bolster the rotation and both gambles fizzled. Ortiz was 3-6 in 13 starts and was cut on July 30, while Hampton went 7-10 in 21 outings before tearing a rotator cuff in his shoulder in August.
The offense was also subpar, ranking 27th in runs scored (3.97 per game) and 25th in on-base percentage (.319).
Leadoff man Michael Bourn hit .285 and led the NL with 61 stolen bases and cleanup hitter Carlos Lee ranked 10th in the NL with 102 RBIs.
But slugger Lance Berkman, another holdover from the World Series team with Oswalt, hit .274 with 25 homers and 80 RBIs, among the lowest numbers of his career. Kaz Matsui, signed through next season, hit only .250. Miguel Tejada, who will become a free agent, hit .313 for the season, but slumped in August and grounded into 29 double plays in 2009.
Late last season, the Astros got glimpses of young players who will contribute next season. Rookie Bud Norris went 6-3 in 10 starts and will compete for a spot in the rotation at spring training, and infielders Tommy Manzella and Edwin Maysonet will push for playing time.
The Astros interviewed 10 candidates, with Mills, Acta and Clark among those considered finalists. Clark was guaranteed a position on Houston's staff if he was not hired as the manager.
Mills served as the Philadelphia Phillies' first-base coach from 1997-2000, when Francona was the manager. Current Astros general manager Ed Wade was the Phillies' GM from 1998-2005 -- and he fired Francona, Mills and three other coaches.
After leaving the Phillies, Mills served as an advance scout for the Cubs (2001) and was the bench coach in Montreal in 2003. The Red Sox hired him in January 2004.