The company will accept virtual currency Hotel bookings only and limit trial transactions only on their US sites.
But one Bitcoin watcher told the BBC this was a "big step" for the currency.
Expedia's announcement comes after a difficult few months for Bitcoin. security concerns.
Smaller online travel sites accept virtual currencies, including Travel Keys and CheapAir, but Expedia was the first major company to adopt Bitcoin.
Emily Spaven, managing editor of Bitcoin news site CoinDesk, told the BBC the move was "brilliant news" and "brought the digital currency to the popular market."
In a statement, Expedia's global vice president, Michael Gulmann, said the company was in a "unique position" to "complete planning and booking for our customers and partners using state-of-the-art payment technology."