Despite having run favored Dialed In to a head in the Florida Derby (gr. I), Shackleford was dismissed at odds of 23.1-1 for the Kentucky Derby Presented by Yum! Brands (gr. I). Clearly the bettors had concluded it was unlikely a front-running son of Forestry could still be ahead at the end of a mile-and-a-quarter contest that appeared to be loaded with speed. In the event, they were proved right, but only just. Having been allowed to set surprisingly soft fractions, Shackleford surged clear in the stretch. After briefly appearing as if he might cause an upset, he was headed by eventual winner Animal Kingdom at the furlong marker, then faded to finish a gallant fourth.
For the Preakness Stakes (gr. I), Shackleford was still relatively friendless before the race at odds of 12.6-1. His bid appeared doomed when he and the speedy Flashpoint zipped through an opening quarter in 22.69, but the pair then steadied the pace considerably. When Flashpoint compounded just after three-quarters of a mile, Shackleford was left clear, and after shrugging off some early challengers, he had just enough left to hold the hard-charging Animal Kingdom by ½-length.