It's a rare look into the life of the third president of the United States.
"I was mining the archives at Monticello this summer," McDonald told CBS This Morning Co-Anchor Russ Mitchell. "I saw a curious looking note card in the file. I looked it up and there they were."
The University of Virginia did not realize what it had.
McDonald said the scrapbooks were thought to have been compiled by Jefferson's granddaughters. However, he said he and his collaborator verified that Jefferson compiled them.
McDonald said he found thousands of clippings from newspapers all over the East Coast that were cut between 1801 and 1809 - the years of Jefferson's presidency.
"There are poems, bits of news about the 4th of July, politics, exploration, education and architecture," McDonald said. "They represent the breadth of Jefferson's vision and his interests."
He said the books reveal a sentimental side of Jefferson - who is often thought of as a man of reason - in a section devoted to his daughter Maria, who died at age 26 in 1804.
"[Jefferson] was criticized for not mourning his daughter," McDonald said. "But he commemorated her life in these scrapbooks."
McDonald said that contrary to many accounts, Jefferson did have a warm side, as evidenced by the presence of articles mocking Jefferson in the scrapbook.
"To imagine Jefferson clipping these out of the newspaper and perhaps chuckling out of his breath and pasting them down into scrapbooks is a different side of him," McDonald said.
He said he hopes to publish a scholarly article that will verify Jefferson's connection to the scrapbooks.
"We hope to be able to edit the books and publish them so others will be able to learn more about Jefferson," McDonald said. "It's a great find. Just a super discovery."