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Rejection
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Mother hamsters may reject their pups, thus leaving them open as a viable option for food. If a pup was born outside the mother hamsters nesting area or if it is a runt, a mother hamster may reject it. Also, if a mother smells a human on her pup in the first two weeks, she may reject it.
Feeling Threatened
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A mother hamster may be overwhelmed and shocked by all her new baby pups and as a means of comforting herself may consume the pups in an attempt to remove the threat.
Nutrients
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Whatever species, the gestation period is taxing on a body. After giving birth, a mother hamster's body may send signals that she needs more protein and nutrients and the only viable option may be her pups.
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Will Mother Hamsters Eat Their Babies?
There is no known reason why mother hamsters eat their pups. There are many theories based on close observation that range from a need for protein and nutrients after birth to feelings of threat from the pups by the mother.