Apple seeds do contain cyanide, a deadly poison. But this shouldn't stop you from enjoying apples, because the quantity of cyanide in the seeds is minute. Even if you were to swallow hundreds of seeds, the cyanide would pass through your digestive tract intact because it is encased by the seed's hard shell, which is impervious to the effects of both normal cooking and gastric juices.
Certain other seeds, including those of apricots and peaches, also contain traces of cyanide in their kernels. Since these seeds do occasionally split open, the eater is often exposed to the cyanide. The quantity of poison in one split seed, however, isn't a serious threat to a healthy person.
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