In 2003 Wilson was drafted in the second round (26 pick overall) of the 2003 NFL Draft by the New England Patriots. In his rookie season he started 15 and played in all 16 of the Patriots regular season games at the free safety position. He had a huge impact on improving the Patriots secondary as he totaled on the year 61 total tackles and 4 interceptions. His first career NFL interception came in the only game that he did not start that year, the season opener vs the Buffalo Bills... In the 2003 postseason he started in all three of the Patriots postseason victory's. In the Super Bowl game vs the Carolina Panthers he pulled a hamstring in the second half of the game and had to sit out the rest of the game. Ironically, shortly as Wilson left the game the highest scoring quarter in Super Bowl history began... Some honors he received for his exceptional rookie season in 2003 included being named to the ESPN.com’s All Rookie Team and to USA Today’s All Joe Team.
The 2004 season for Wilson was almost a repeat of 2003 as he played in 15 of the Patriots regular season games and started 14. He once again intercepted 4 passes (best on team) and upped his total tackles by six, finishing the regular season with 67 total tackles. He was named the AFC Defensive Player of the Month for September.... Starting all the Patriots postseason games at safety in 2004, Wilson had two postseason interceptions (both in the AFC Championship game) and one fumble recovery. Once again, Wilson did not completely finish the postseason as he broke his arm in the second half of the Patriots Super Bowl XXXIX victory over the Philadelphia Eagles.
In 2005, Wilson played in and started all 16 of the Patriots regular season games (also started both of the Pat's postseason games). In a sort of down year for him he made 68 total tackles but only made one interception.
In 2006, he missed all but four games of the Patriots season. On December 6, 2006, the Patriots placed Wilson on the injury reserve list ending his season.