The run honors firefighter Stephen Siller, who ran three miles in full gear through the Brooklyn Battery Tunnel after being told he wasn't allowed to drive through during the terror attacks.
Siller later died rescuing people from the towers.
This year's run comes a day after a truck carrying 18,000 shirts and materials for the race caught fire and destroyed or damaged all that was inside.
Siller's brother, Russ, says the incident won't stop the race.
"You start to prioritize and you realize what's a small problem and what's a big problem and so you know, shirts burning is not a big problem, rain is not a big problem -- 9/11 was a big problem," Siller said.
Organizers expect about 20,000 runners to come out for the race.
The Brooklyn Battery Tunnel will be closed to traffic today until 3 p.m.