He served as New England's defensive backs coach for five seasons before being named defensive coordinator on Feb. 12, 2005. In his first five seasons with the Patriots, he tutored a secondary that earned five Pro Bowl selections and evolved into one of the NFL's most successful defensive backfields.

The performance of the Patriots secondary and its ability to succeed despite key injuries earned high acclaim in 2004. Due to injuries, Mangini had to utilize nine different starters and converted a linebacker and a wide receiver into defensive backs as the Patriots won their third Super Bowl in four seasons. Following season-ending injuries to each of the opening-day starting cornerbacks, second-year pro Asante Samuel and undrafted rookie Randall Gay stepped in and started 23 games between them, including all three playoff contests. At safety, Rodney Harrison provided strong veteran leadership to the young unit, while Eugene Wilson's versatility allowed him to contribute at safety and cornerback.

Mangini's tutelage helped wide receiver Troy Brown, in his 12th season in New England, learn to play cornerback when the secondary was depleted by injuries. Brown responded by tying for second on the team with three interceptions and recorded 17 tackles to go along with his 17 receptions on offense. Linebacker Don Davis was also used in the secondary, starting at safety for the final two games of the regular season.

Despite the personnel changes in the secondary, the unit was a crucial part of the Patriots success, especially in the playoffs. During the regular season, seven different members of the secondary recorded at least one interception, while defensive backs accounted for half of the team's 36 takeaways. In the postseason, defensive backs recorded six interceptions in three games, with Harrison accounting for four picks, including one returned for a touchdown.

The secondary was an integral part of a dominating Patriots defense that led the NFL in 2003 by allowing a franchise-record 14.9 points per game as the Patriots ended the season with 15 consecutive wins and claimed the Super Bowl XXXVIII title. New England's pass defense led the NFL in four key categories – interceptions (29), fewest touchdown receptions allowed (11), opponents' passer rating (56.2) and pass defl ections (121). The Patriots' 29 interceptions were the second most in franchise history and the most by a Patriots team in 40 years (1963, 31 picks). In the entire 2003 regular season, the Patriots gave up just one pass play of over 50 yards and did not give up a rushing play longer than 23 yards.

Mangini was able to help guide the secondary to success in 2003 despite the fact that only one of the top five defensive backs was with the team in 2002. In all, the 2003 secondary produced 21 interceptions and 73 pass defenses – an improvement of 13 interceptions and 41 pass defl ections over the 2002 unit. New England's secondary also played a key part in the Patriots' postseason success, with Ty Law recording three interceptions in the AFC Championship Game and Harrison picking off a pair of postseason passes.

In 2002, the secondary produced three of the team's top five tacklers, with Lawyer Milloy (91 tackles), Victor Green (84) and Ty Law (77). Collectively, the defense forced 29 turnovers, including 18 interceptions. Nineteen of those 29 turnovers were credited to the secondary.

In 2001, the Patriots defense was again among the stingiest in franchise history and one of the most opportunistic in the NFL. As a unit, the defense allowed just 17 points per game, a result of many potential opponent scoring drives ending in turnovers. The Patriots recorded 35 takeaways, including 22 interceptions (12 more than in 2000). Five of those 22 interceptions were returned for touchdowns, which led the NFL, and defensive backs scored all five touchdowns. Law added another interception in Super Bowl XXXVI that he returned 47 yards for a touchdown.

Mangini joined the Patriots after three seasons (1997- 99) as the defensive assistant/quality control coach for the New York Jets. During that time, he worked closely with Belichick, who was the Jets assistant head coach/ secondary. Mangini was also responsible for advance opponent film breakdowns and analysis. In 1999, the Jets defense ranked third in the AFC with 24 interceptions, the team's highest total since 1969 (29). The defensive backs recorded 18 of those 24 interceptions. In 1998, the Jets defense surrendered just 16.6 points per game, ranking third in franchise history and helping the Jets to a 12-4 overall record and their first division title.

Mangini's first coaching opportunity came in 1995 as an assistant on Belichick's staff in Cleveland. Ted Marchibroda retained him when the franchise moved to Baltimore in 1996, working as a quality control/offensive assistant.