Mats Hafstroem, owner of the Djurparken Zoo in Helsingborg, said someone broke into the facility late Monday or early Tuesday and stole the two snakes. One is yellow and the other striped green, TheLocal.se said.
The burglars ransacked other parts of the zoo, probably looking for more snakes. Hafstroem said veterinarians recently noted 15 snakes of the breed were hatched but only two were put on public display.
The burglars broke into the terrarium where the reptiles were kept and even broke into the zoo's office.
"They must have been looking for the other 13," he said. "It's extremely rare that pit vipers are born in captivity."
Hafstroem assured residents living by the zoo none of the snakes escaped and even if they did, Asian pit vipers can't survive in Sweden's cold climate. They are native to southern Asia.
The pit viper, Trimeresurus, is nicknamed the 100 pace snake -- because those bitten don't make it 100 paces before dropping dead once they're bitten.
Hafstroem said he hopes the publicity the break-in gets will make it more difficult for the thieves to sell the snakes.