I just saw the question Facultative Cannibalism? on the biology web site, and I recalled hearing the tom cats, will kill house cat kittens.
Will neutering a male cat stop it from killing kittens it did not father?
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The only reason male felids do that is related to sex. Killing the kittens forces the female to go into heat again, plus there might be some programmed instinctual drive to kill kittens that are not partly yours (beyond bringing the female into heat- to ensure your genes are passed on). That happens with large cats, I do not know if it happens with house cats or not. Once the male is neutered there is no more testosterone being produced (granted whatever was already in the bloodstream takes some time to go away) and I would be surprised if this behavior wasn't tied to the presence of sex hormones.