No, Obama did not refuse to put his hand on his heart during the pledge of allegiance.

In late 2007 an email circulated with a photo of Senator Obama with his hands clasped just below his waste; beside him were Bill Richardson and Hillary Clinton with their hands on their hearts. Text accompanying the photo claimed Obama "refused not only to put his hand on his heart during the pledge of allegiance, but refused to say the pledge."

That photo was not taken during the Pledge of Allegiance, however - it was taken during the singing of the Star-Spangled Banner. [1]

"My grandfather taught me how to say the Pledge of Allegiance when I was 2," Obama said in Burlington, Iowa. "During the Pledge of Allegiance, you put your hand over your heart. During the national anthem, you sing." [2]

Here is a video showing Obama leading the U.S. Senate in the Pledge of Allegiance, with his hand on his heart:

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[1] ABC News. Obama Out of Tune? November 11, 2007

[2] Adair, Bill. E-mail Assailing Obama's Patriotism Misses Mark St. Petersburg Times November 9, 2007

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Additional Resources:

Snopes.com: Barack Obama and the National Anthem

FactCheck.org: Sliming Obama January 10, 2008

Politifact.com: Photo was taken during anthem, not pledge