In 2006 a serious leg injury halted his season. During the final moments of the St Kilda vs West Coast Eagles game in Round 18, Maguire collided with Tyson Stenglein causing a break to both his tibia and fibula. His injury was likened to that of Richmond's Nathan Brown, but it was soon revealed to be less severe. In the days following the incident, Maguire had a rod inserted into his leg and the club was optimistic he could make his comeback (without any complications) as soon as Round 1, 2007. But soon after Maguire was diagnosed with Compartment syndrome and required a further eight operations to relieve him of the pain and swelling. He suffered complications with compartment syndrome in his calf and spent 21 days in hospital. Doctors had to cut into his calf numerous times to clear the build-up of blood, with ever-increasing difficulty in repairing the wound.