After a strong start to the 2006 season, Hayes ruptured his anterior cruciate ligament against the Kangaroos in Round 9, requiring a minor knee reconstruction which sidelined him until the 2007 season. In just his fifth game back in the 2007 season he suffered a broken collarbone, sidelining him for three weeks, although he managed to come back and play 19 games for the year.
Hayes played 25 games in 2010, including four finals, and received a number of accolades for his performances during the season:
Trevor Barker medallist for St Kilda's best & fairest player in 2010.
2010 Norm Smith Medallist (1st Grand Final).
St Kilda's player of the finals series (jointly with Zac Dawson).
Hayes injured his left ACL early in the 2011 season and did not play the rest of the year.
Hayes played all games in 2012 and won his third Trevor Barker Medal as St Kilda's best & fairest player for the season. He had a fantastic season and made a brilliant recovery from the ACL injury from 2011. He played his 250th game in Round 9 against eventual premiers Sydney, gaining 25 disposals in a 28-point win for the Saints.
On 15 July 2014, Hayes announced his retirement in front of all his teammates and family. Out of respect his teammates wore t-shirts with the hashtag #ilovelenny. At the time of his retirement, Hayes held the VFL/AFL all-time record for most tackles in a career, having lain 1,496 tackles at an average of 5.04 per game; he still holds the record as of 19 September 2014.