Baby chicks get diarrhea for several reasons, ranging from completely harmless digestive patterns to infections that need quick treatment. The most common culprits are stress from shipping or temperature changes, dietary issues, a blocked vent condition called “pasty butt,” and a parasite called coccidia. Telling the difference between normal and abnormal droppings is the first step to figuring out what’s going on.
It Might Not Be Diarrhea at All
Chickens have two types of droppings, and one of them looks alarmingly like diarrhea even when everything is perfectly fine. Several times a day, a pouch in the digestive tract called the cecum empties its contents, producing what’s known as cecal droppings. These are darker, mushier, and significantly smellier than regular droppings. The color can range from yellow to nearly black, and the darker they are, the worse they smell. This is actually a sign of a healthy digestive system.
Chicks also produce wetter droppings when they’re drinking more water than usual, which happens in warm brooders or during hot weather. If your chick is active, eating well, and the loose droppings appear only occasionally between firmer ones, you’re likely looking at normal cecal poop or extra water intake rather than true diarrhea.
True diarrhea is persistent, watery, and often accompanied by other signs: lethargy, loss of appetite, fluffed-up feathers, or a chick that stands apart from the rest. Color matters too. Yellow and foamy droppings can signal parasites, infection, or kidney problems. Dark green and watery droppings often appear when a chick has stopped eating. Any blood or orange tinge is a red flag that warrants immediate attention.
Pasty Butt: The Most Common Issue in New Chicks
If you just brought your chicks home, the most likely problem is pasty butt, where droppings stick to and dry over the vent (the opening where droppings come out). This can block the vent entirely, which is life-threatening if not cleared. It’s especially common in the first week of life.
The biggest cause is poorly digestible ingredients in the feed. A young chick’s digestive system doesn’t yet produce enough of its own enzymes to fully break down solid food, since it just transitioned from absorbing the egg yolk. Shipping stress, temperature swings in the brooder, and being too hot or too cold all make it worse. If multiple chicks in your brooder are pasting, check your temperature first.
To clean pasty butt safely, hold the chick gently and run its rear end under warm (not hot) water until the dried material softens. Then use a cotton swab in a downward motion to work it free. Never pull dried droppings off, as you’ll tear the skin and feathers. If the mass is really cemented on, dab a small amount of vegetable oil onto it first to soften it before using warm water. Make sure the chick is completely dry before returning it to the brooder, since wet chicks chill quickly. A thin layer of petroleum jelly or vegetable oil on the clean vent area can help prevent it from happening again.
Coccidiosis: The Biggest Infectious Threat
Coccidiosis is the most dangerous and most common parasitic disease in baby chicks. It’s caused by a microscopic parasite called Eimeria that chicks pick up by pecking at contaminated litter, feed, or water. Once swallowed, the parasites invade the cells lining the intestine and multiply rapidly inside them, eventually bursting out and destroying those cells in the process. This cycle repeats multiple times, causing progressively more damage to the gut wall.
As the intestinal lining breaks down, the chick loses its ability to absorb nutrients. Fluids and proteins leak into the intestine, producing watery, sometimes bloody or mucus-streaked droppings. The damaged gut also becomes vulnerable to secondary bacterial infections that can make things even worse. Symptoms typically appear between 3 and 8 weeks of age and include watery or bloody droppings, weight loss, lethargy, ruffled feathers, and in severe cases, death.
If you suspect coccidiosis, treatment with amprolium (sold under brand names like Corid) added to the drinking water is the standard approach. Amprolium works by starving the parasite of a vitamin it needs to reproduce, effectively making it sterile. Treatment typically runs 3 to 5 days at the higher dose, followed by 1 to 2 weeks at a lower dose, and during this time the medicated water should be the only water source available.
Medicated chick starter feed contains a low level of amprolium designed to let chicks build immunity gradually while keeping the parasite from overwhelming their system. It reduces the risk of coccidiosis but cannot fully prevent an outbreak, especially in damp or dirty brooder conditions. If your chicks were vaccinated for coccidiosis at the hatchery, do not use medicated feed, as the amprolium can interfere with the vaccine.
Bacterial Infections and Pullorum Disease
Bacterial infections can also cause diarrhea in young chicks. One historically significant disease is pullorum, caused by a strain of Salmonella that is specifically adapted to poultry. It produces white, chalky diarrhea (which is how it got its old name, “bacillary white diarrhea”) along with depression, loss of appetite, and high mortality. Pullorum has been largely eradicated from commercial flocks through decades of testing programs, but it can still appear in backyard flocks sourced from untested birds.
Other bacteria, including E. coli and Clostridium, can cause loose or foul-smelling droppings, especially when chicks are already stressed or have gut damage from another condition like coccidiosis. Dirty water, soiled bedding, and overcrowding all increase the risk of bacterial problems.
Stress and Diet-Related Causes
Shipping stress is one of the most common reasons newly arrived chicks have loose droppings. The combination of temperature fluctuations, dehydration, and the physical stress of transport can disrupt digestion for the first day or two. This usually resolves on its own once chicks are warm, hydrated, and eating consistently.
A teaspoon of sugar per quart of warm water (around 98°F) for the first few hours after arrival helps chicks recover from shipping stress. After the first 4 hours, switch back to plain warm water. Too much sugar or electrolyte solution beyond that initial period can itself cause loose stools.
Dietary protein that’s too high for a chick’s age, sudden feed changes, or treats and scraps introduced too early can all trigger diarrhea. Stick with a complete chick starter feed for at least the first several weeks. Temperature in the brooder matters too: chicks that are too cold can’t digest food properly, and chicks that are too hot drink excessively, both of which produce wetter droppings.
How to Tell What’s Causing the Problem
Start by looking at the droppings and the chick’s behavior together:
- Occasional smelly, mushy droppings with an otherwise active chick: normal cecal droppings.
- Droppings stuck over the vent in a chick under 2 weeks old: pasty butt. Clean it promptly and check your brooder temperature.
- Watery or bloody droppings with lethargy in a chick 3 to 8 weeks old: suspect coccidiosis, especially if the litter has been damp.
- White, chalky diarrhea with depression and high flock mortality: possible bacterial infection like pullorum.
- Loose droppings in newly arrived chicks that clear up within a day or two: shipping stress.
Keeping Droppings Normal Going Forward
Clean, dry bedding is the single most important factor in preventing diarrhea in baby chicks. Wet litter breeds coccidia and harmful bacteria faster than almost anything else. Change bedding frequently and make sure waterers aren’t spilling onto the litter.
Keep the brooder at the right temperature for your chicks’ age, starting around 95°F in the first week and reducing by about 5 degrees each week. If chicks are huddled together, they’re too cold. If they’re spread to the edges avoiding the heat source, they’re too warm. Provide clean, fresh water at all times and use a complete chick starter feed as their sole diet. Avoid kitchen scraps, garden treats, or excessive supplements during the first few weeks while their digestive systems are still maturing.