The rare West African dwarf crocodiles, measuring 30 centimetres when young, can grow to 1.8 metres, police said.
They were taken from their cage at Leipzig Zoo at the weekend during visiting hours.
"This may have been some kind of test of courage, but the animals aren't going to be a good Christmas present," police spokesman Thorsten Dressler said.
The reptiles, an endangered species, were among five born at the zoo, which had been proud about breeding them in captivity.
"We just hope they are treated right and don't end up in the sewage system," said Kathleen Raschke, spokeswoman for the zoo.
The thief faces charges of threatening public safety and endangering the lives of a protected species.