Pujols leads the NL, while Phillies first baseman Ryan Howard moved into the No. 2 spot, with Brewers first baseman Prince Fielder dropping to third.
Hamilton is followed in the AL poll by Rays third baseman Evan Longoria in second place. Red Sox designated hitter David Ortiz holds the third spot.
More than 20 million ballots have been distributed to 30 Major League ballparks in conjunction with home game voting promotions. Fans are also encouraged to vote up to 25 times on MLB.com.
The 2009 State Farm Home Run Derby will be broadcast live on ESPN at 8 p.m. ET on July 13.
Amy Brittain is an associate reporter with MLB.com. This story was not subject to the approval of Major League Baseball or its clubs.