The Metropolitan Police said the two signed prints, "Pyronin Y" and "Oleoylsarcosin," were taken from the Exhibitionist Gallery in west London in the early hours of Monday by a thief who forced the gallery doors. The works are among Hirst's series of "spot" pieces, covered in multicolored dots.
Gallery manager Nathan Engelbrecht said the thieves appeared to have targeted the Hirst works.
A security-camera image released by the gallery shows a figure wearing gloves carrying a large framed print toward the exit.
"The thief left other works in the gallery, just taking the prints. The store room had not been touched at all. The spot prints are the most recognizable Hirst works. The others we had were left behind."
Detective Sgt. Jon Lightfoot appealed for witnesses who might have seen a dark-colored hatchback car with polka-dot artworks in the back driving from the area to come forward.
Hirst, 48, is one of Britain's best-known and wealthiest living artists, famous for his diamond skulls, pickled sharks and rotting animal installations as well as his paintings and prints. In 2008, a Sotheby's auction of his work netted almost $200 million, a record for a living artist.
A spokesman for Hirst declined to comment on the theft.