Any time you get a new horse it is wise to practice quarantine with it prior to introducing it to any resident equines. This is especially true when your new horse comes from a questionable source such as an auction, feedlot, kill pen, horse dealer/trader etc. Prior to getting your new horse you should question the folks as to if there is any potential sickness that you should be aware of. If you can get a vet check done, that is lovely. However, lets assume you are just taking the horse in with no information. I will tell you what I do, and what works for me, but please remember that I am not a vet and use your own discretion because ultimately you are the one responsible for your horse.
Before your new horse arrives, you should ask the folks you are getting him from if there are any sicknesses that you need to be aware of. You should already have a vet before your new horse arrives and it is a good idea to give your vet a heads up that you are getting a new horse. When planning for the arrival of your horse, think about transportation. He will be hauling in what is called a "dirty load", which means the horses have not gone through quarantine. He should not haul with horses from other locations and the trailer will need to be disinfected after his use. If other horses are going to haul with yours, then you should all share contact information in case one of the horses turns out to be sick.
Your horse will need an area to quarantine in that is separate from all other equines and preferably doesn't even share a fence line with them. The first and most key issue is that the new horse must be kept separate from other equines. Please do not put your new horse in with resident horses, donkeys or mules. The new horse should not be able to reach any other horses, so that means that he cannot share a fence line. Frankly the further you can put him from your other horses the better. He will need his own water bucket and food containers. He should have his own manure fork and you should plan for his manure to also be kept away from your other horses. Please notify anyone else who shares the property that the new horse is under quarantine.
Upon arrival you should make a close inspection of your new horse and mark notes down on paper and via camera. Do you have the right horse? What is the approximate weight of your new horse? Does he appear healthy and alert? Does he have any snot and if so what is the amount and color of it? Is the horse coughing? What is the horse's temperature? Is he dehydrated? If he so graces you, what is the consistance of his poop? Was your horse hauled with other horses? If so, take a quick look at them if possible. Are there any documents that come with your horse? If so, make sure to get them before the hauler leaves. After you get your new horse settled, it is generally best to give him his hay, water, and then just let him relax.
Do not introduce your new horse to your other horses, even if they are calling to each other and seem interested. Keep curious people, kids, dogs, and other animals away from him since some sicknesses can be transported back to other horses by these means. When you are feeding or working with your horses; work with your previous horses first and the new horse last. Disinfect yourself and your clothing after working with the new horse and don't forget your boots! Do not share grooming supplies, tack or other equipment between your new horse and your others.
While your new horse is in quarantine you must still take care of him and provide him with all normal care. He must still be groomed, cleaned, handled etc. If he has any secondary issues (rain rot, cuts, whatever) those still need to be treated. His feet still need to be trimmed. If you need to have a vet, farrier, etc work with your horse please make sure to tell them ahead of time that the horse is in quarantine. They will likely want to schedule your appointment as the last one of the day and they may charge you a little more for the extra time and precautions that they will need to take. Do not give vaccines during this period.
While your horse is in quarantine you should be keeping careful watch of him. Check his temperature daily (if not more often) if you suspect he may actually be ill. Take full body pictures at least weekly because you may not notice weight loss or gain since you are seeing your horse daily and the changes may happen slowly. If your horse is showing active symptoms of being sick (temperature, coughing, swelling, extended periods of lethargy etc) then you need to call your vet. Your vet may decide that it is not something that needs treatment, but you need to at least have that discussion. Do not give your horse antibiotics without talking to your vet.
How long to quarantine will depend on several factors, but the most important ones are how your horse is doing and how the other horses from the same trailer are doing. The most common sickness that folks worry about quarantining against is Strangles. Strangles has an incubation period of 3-14 days. Therefore I always recommend that folks quarantine for at least 16 days, but more is better. That is if your horse appears perfectly healthy. If your horse appears sick, you will want to quarantine for a couple weeks after all signs of illness have passed, or until your vet gives you the all-clear. If your horse does come down with Strangles, then you will want at least one clean culture from your vet prior to stopping quarantine.
If you get two (or more) horses from the same place at the same time, it is generally not a big deal for them to share quarantine. However, should your quarantining horse come into contact with another horse during it's quarantine period, that other horse should also be put into quarantine. It is best to quarantine them separately if possible.
The following things should go without saying, but I will say them anyways since I have seen them all done before. While your horse is quarantining do not take him to: shows, events, trail riding, camping, fair, training or anywhere else that other horses are. Do not haul him in to the vet or farrier without calling them first and checking that it is okay and seeing if there are any procedures that they want you to follow. If anyone else is going to be hauling your horse for any reason, tell them that your horse is in quarantine; your horse will need to be hauled alone and their trailer will need to be disinfected after use. Do not bring home tack to try on your horse and then return it. Do not take food that your quarantining horse has refused or wasted and give it to another equine. Do not use paste wormer, bute, etc on another horse after you have already used it to dose your quarantining horse. Do not breed your horse while it is in quarantine. If your new horse is a nurse mare, do not foster a foal onto her during quarantine unless absolutely necessary. If your quarantining horse is a mare who gives birth while in quarantine, the foal should stay with its mother in quarantine unless otherwise advised by a vet.