Q: What is quarantine and when should I quarantine my flock?
A: In your backyard flock, quarantine is the act of isolating a chicken or chickens who has been potentially or actually exposed to contagious illness from the rest of your flock.
When you introduce new chickens into your established flock, for example, you must quarantine the new chickens for four weeks from the rest of your flock. You don't want them to share feeders, waterers, or even the same air. You also want to be careful not to carry anything between the flocks on your person (on your shoes, for example) during this time.
Hens in the Hen Pen Chicken run isolating from the existing flock.
The four weeks of quarantine gives you the opportunity to determine if the new chickens are ill with a virus or bacteria, or if they're carrying something like lice, mites, or worms. You'll also want to quarantine members of your flock that have participated in a poultry show, where s/he may have been exposed to something carried in by another chicken at the exhibition
You quarantine because it's easier and less expensive to treat your three new birds for mites than it is to treat your whole flock of 18! And in the case of serious illness, it's much preferred to lose three chickens than to lose 18. You also quarantine because your own flock may have immunity to endemic illnesses in your area, while your new birds may not have the same resistance. They'll need a little time, and it's best to give them that time when they're not facing the social stress of finding their place in the pecking order at the same time.
Four weeks seems like a long time, and some are tempted to cut quarantine short. Don't do that! The reason is that most illnesses have an incubation period, which is the period of time where your bird is infected, but during which s/he's not yet showing any symptoms. So just because you've observed your new birds for a week and see no signs of illness doesn't mean it's safe to put them together with the rest of your flock. Four weeks is the proper amount of time for a quarantine.
Once the quarantine is over, you can then proceed to introducing your new birds to the established flock.