In 1895 a fire burned all but the brick foundations of the building. First hand accounts note that students worked to remove the educational materials that they could before the fire engulfed the building. Because the dome and the additional annex of the building were entirely built of wood they were completely destroyed in the fire.
The Rotunda was rebuilt from 1898-1899 by McKim, Mead, and White of New York. The design was modified slightly by Stanford White. White included a fireproof dome that was larger than Jefferson's original and did not rebuild the Annex.
In 1972 the US Bicentennial Committee sought to restore the Rotunda to Jefferson's original design. The dome was restored to three stories, the skylight was given a simpler design, and the interior design choices made by White in 1899 were restored to the original design. The construction was completed by 1976 for the Bicentennial.