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I think answers to this question can be agnostic of pet species. So I am asking the general question, if my pet who is member of my family has a litter should I avoid touching them and getting my scent on them? If so for how long should I avoid touching them?

I have heard that if you touch a wild baby animal it's mother may reject it, and your touch may lead to the babies death. Does the same apply to baby pets?

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It depends on the species. I know for some you are encouraged to touch from birth, some you must leave it for a few days, birds for example. In my experience, if your pet feels safe, then you may touch the babies. Generally you should follow your pet's lead - link.

I left my cat's babies 3 or so days before properly handling, because she was nervous, although I did quickly touch the babies as they were being born, keeping them near her etc. For the record, this cat was semi-wild and had not lived with us very long, and she was fine. With my rat, the babies were born at 9am and I handled them at 10, as soon as I was sure she was finished - it was fine because my rat 100% trusted me, and with rats it's necessary to handle ASAP to ensure they are used to humans and are as friendly as possible.

It is important to at least touch the new babies to check them over for birth defects.

When wild animals abandon babies, it's usually because the nest has been disturbed, not solely because the baby has been touched. The rule about touching doesn't apply if your pet trusts you, because your scent isn't a threat, although it absolutely depends on the individual animal.

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