The following information should be used for diagnostic purposes only, so please consult a vet whenever you feel your chickens may be ill.
As you will see, many diseases that can effect your flock can be prevented with vaccinations but the expense of such treatment may seem excessive if you are only managing a few birds for your own egg supply. If you are not too attached to your birds, you may find it more cost effective to simply slaughter the sick birds and buy new chicks rather than maintain a vaccination program for your whole flock.
One thing to consider is that your backyard flock (especially in city regions) is more isolated than birds raised in rural areas. This can limit the exposure to chicken-specific diseases.
With the recent outbreaks of mutated forms of Avian flu among humans around the world, this one disease that many new backyard flock owners are curious about. Avian flu (or just bird flu) is really just another form of flu and it will effect your chickens in the same way.
Chickens with bird flu usually have respiratory symptoms, like wheezing or coughing and their combs and wattles may get discolored. Ill birds will also be lethargic and off their feed. If you suspect your chickens have the flu, you can still use their eggs (though they will likely have a reduced output until their are better). All eggs should be well cooked, and you should be doubly careful to wash your hands after you handle them.
Most chickens who get bird flu will recover on their own, and you can also get them vaccinated if you find that they catch it frequently.
Marek's is one of the more serious diseases that your chickens can get, and it's usually fatal. It's a form of herpes that effects the nerves and sometimes the internal organs of your birds. The most commonly seen symptom is paralysis in the wings or legs, and sometimes your chicks will have strangely colored or shaped eyes. The disease can spread from one farm to another through dust in the air, so you don't actually have to have contact with a diseased bird in order to spread it.
The best way to protect your flock against Marek's is with vaccination of your chicks. Young chicks only need one treatment, and some chick seller's will have already vaccinated their chicks before sale. If not, it is something you can do yourself if you don't mind giving needles to your birds. Once they reach 5 months of age, most chicks would have already developed their own immunity to the disease.
Do not confuse this with the chicken pox disease that humans get. Chickens can get their own version of pox, and it can be spread by biting insects or just through the air if infected chickens are nearby. Pox spread by insect bite (usually mosquitoes) appears as sores and black lesions on your chicken's combs or wattles. While the bird has the disease, you'll get far fewer eggs and your chickens will be pretty unhappy. But otherwise they can usually get over it within a few weeks on their own.
But if they get pox in the inhaled version, it can be more serious and show as sores inside the mouth and other respiratory problems. You can get your chickens vaccinated for pox, just like with the other diseases.
Salmonella is more of a threat to you and others who eat your backyard eggs, rather than the chickens themselves so it really needs to be included here. Though you have likely heard of salmonella risks with raw eggs, don't forget that your backyard situation is much different than a factory farm. As long as you keep your chicken area clean, there will be a minimal problem with salmonella.
That does not mean your chickens and eggs will be 100% salmonella free. The bacteria is mainly found on the outside of your eggs, so you should always wash your eggs immediately after collecting and store them in the fridge. Then give your hands a good wash as well. When it comes time to use your eggs, make sure you cook them thoroughly. If you wish to use the eggs raw (such as in an egg nog), that doesn't mean you will automatically get sick. With proper cleaning first, the risk is still minimal.
Salmonella symptoms in humans are classic "food poisoning" symptoms, such as nausea, vomiting, diarrhea and possibly fever. If your chickens become ill, you'll see lethargy, diarrhea and a lack of appetite.
Coccidiosis is a disease or condition caused by internal Coccidia protozoa that naturally live inside of every chicken. If they become too numerous, they will cause illness. Most chickens only suffer from this when they are young, under 4 months old typically. After that, they are more immune to the organisms. Many brands of chick mash are medicated to help with this, so you can usually prevent it that way.
Chickens that are suffering from coccidiosis usually don't show many symptoms until they are already quite ill. Watch for young birds that have little energy and running droppings. You can get medication for your chicks but they may already be too sick to treat. Isolate them from your other birds, if possible.
Keep your coop area clean, and change the water frequently to help prevent the spread of this disease.
In this case, worms are small parasites that live inside the intestinal tract of your chickens, not the earthworms you find in the soil. Keeping them in check is an ongoing chore, so don't consider this something you just deal with once or twice. Letting worms get out of hand will leave you with sick chickens and fewer eggs.
They spread via eggs and worms in your chickens droppings, so keeping their run clean is the first step in breaking the worm cycle. Free-range chickens, or birds in a movable pen have an advantage in this regard as they are not kept on the same patch of ground constantly.
There are several worming products that you can use, all with their own duration times and dosages. Some are given monthly and some are given just twice a year. Whether or not you can use the eggs during a worming treatment will depend on the product, so read the instructions carefully. You can also take a natural approach, and add diatomaceous earth to their feed to keep worm populations down. It's not medication, but does need to be provided frequently to kill intestinal worms.
Ticks and Mites
Worms are a problem inside your chickens, but there are plenty of little parasites that can be found on the outside too. A whole range of ticks, mites and fleas can take up residence on your chickens.
They are extremely common, even in very clean conditions. A few mites or ticks won't cause many problems but a large population of these pests can be an issue. They can spread disease, and will eventually effect the chicken by causing a loss of feathers, reduced appetite and various levels of lethargy.
Depending on the specific insect, there are many products you can use to get rid of them. There are several brands of insecticidal dust that can be used inside the coop and in the bedding, and some can be used with the birds themselves. Always check the directions as some products should not be used right on your chickens. And like with worms, you can use diatomaceous earth to help eradicate tick, mite or flea populations a little more naturally.
Some insects are only found on chickens, but various ones are happy to hop from your birds to other animal pets or even people. So if you choose to ignore the problem in your chicken coop, you may end up with a spreading problem inside your house as well.
Basically, keeping your chicken coop clean with fresh bedding and good food is the best defense against most illnesses. If you take good care of your chickens, you'll find that you have little to deal with in terms of parasites or disease.