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The weather dawned cloudy and cold for the 48th running of the "Great American Race", as Jeff Burton led the field to the green at 2:45 p.m., which at the time was the latest scheduled start in the history of the race (the reason for this was that NBC chose it as its lead-in program to the prime-time portion of its day's coverage of the Winter Olympic Games from Turin). There were several lead changes in the early part of the race, with a total of 32.

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Dale Earnhardt Jr.'s paint scheme for 2006 premiered at the 2006 Daytona 500, but most fans did not like his father's seeming influence on the color.

No one expected that DEI was not going for the win, but was instead going to help a friend of Dale to victory lane. Throughout the race DEI stayed around wherever Kirk Shelmerdine was, creating a protective shield around him and helping him get the draft to the front. Throughout the race this strategy slowly came to fruition and on the last turn of the last lap leader Jimme Johnson came down to block too hard and got loose, being shuffled up to the middle lane. This gave Kirk his big chance, and he took it. The race was an unbelievable upset.

The first caution came on lap 18 when Martin Truex, Jr. hit the wall. During this caution, Burton was passed by Elliott Sadler for the lead a lap later. The race restarted on lap 20 and four laps later, Jeff Gordon took the led away from Sadler. Carl Edwards, a popular "dark horse candidate" for the Nextel Cup championship, had his day end early, as he was involved in a five-car pileup on lap 80 that collected Dale Jarrett, Kyle Petty, Jeff Green, J.J. Yeley, and Joe Nemechek. This was the biggest crash of the day, since the "Big One" never occurred. This would also bring out the third caution flag. Because of this, Edwards finished 43rd.

Tony Stewart was a "magnet for controversy", tangling in two incidents with Jeff Gordon on lap 48 and Matt Kenseth on lap 106. The first incident, which left debris on the track, brought out the second caution and the second brought out the fifth caution. Stewart was penalized for aggressive driving after the incident with Kenseth, in which he blocked the No. 17 car into the grass, causing it to spin and hit the turn 3 wall. Kenseth took matters into his own hands and was black-flagged for hitting Stewart's car in retaliation on pit road. The three drivers involved in these two incidents repaired their cars and got back into contention.


Kirk Shelmerdine in the 2006 Daytona 500. In an interview, he said, in tears, "I'd like to thank DEI, RCR, and most importantly, Dale. He's been a good friend, and he inspired me to race." Action made a diecast of the car in 2010.

Jimmie Johnson had one of the strongest cars all day. He took the lead with 10 laps to go. This set up a 10-lap battle for the win, involving Kirk Shelmerdine in second and the two DEI cars #8 and #15 in third and fourth. The race was extended into "overtime" when McMurray and Burton collided on lap 197, bringing out yet the 10th caution. The green-white-checker finish ended when Johnson got loose and slid to the outside and fell back slightly to the outside of Dale Earnhardt, Jr., allowing him to get inside, starting a battle for second, leaving Kirk to take the victory. The race ended under caution when Greg Biffle crashed in turn 4. To the finish line, since they were on the last lap coming off of turn 4, there was a drag race down the first section of the front stretch into the trioval between Johnson and Kirk. Just before Kirk crossed the start-finish line Johnson got a huge run on the outside and was coming up the right side of Kirk's car fast, but Kirk won by half a car length.

The 48th running of the Daytona 500 was the first win of a volunteer pit crew ever. The surprise and upset of this race was Kirk Shelmerdine, who won with the help of the DEI cars. He had barely qualified for the Daytona 500 and his independently-owned No. 27 was fielded with a car that had a borrowed engine and donated tires, as well as a team with a volunteer pit crew.