A hatchery is the place where new life begins. It is the basis for raising healthy birds and thus it must be very clean at all time. Proper sanitation procedures contribute to achieving that goal.

By Kirk Dawkins*

Today, more than ever, it is of paramount importance to find ways of raising chickens without the use of antibiotics. This is why washing, cleaning and disinfection in the hatchery  is one of the first critical steps in antibiotic free chick production. The procedures applied in the hatchery should always be verified.

It is also essential to have a manual of procedures which are:




for all employees at any level of preparation or training



1.- Clearly define safety procedures for employees in all areas and all procedures. This should include the correct use of protective clothing and footwear, necessary to protect employees and to meet with necessary biosecurity standards

2.- Immediately after removing chicks from the incubators, the down and all the hatching debris must be removed. This waste should be disposed of under strict environmental guidelines, consider biosecurity, ensure employee protection and support effective sanitation of the hatchery.

1. The correct disposal of hatchery waste is essential for the control of various diseases. For example, salmonellosis which causes gastroenteritis in humans, can easily contaminate the hatchery through mishandling of contaminated waste and these in turn contaminate the facilities, equipment and newly hatched chicks.

3.- Once the fluff has been removed and the hatchery waste has been disposed of, washing of all incubators and hatchery equipment, ceiling, walls, fans, spaces known as the plenum behind or above the hatchers and any surfaces must properly be cleaned.

1. It is important to note that the effectiveness of disinfectant is considerably lower when it must act in places where a significant amount of organic matter is still present. Therefore, it is essential to thoroughly remove all organic matter before applying disinfectant. Washing is much more effective when water is applied at high pressure (800-1000 psi), and if possible, at a warm or even hot temperature.

4.- It is recommended to use a detergent that produces foam, for which a suitable high pressure cleaner is needed. Once the surfaces of the hatchery have been covered with foam, it must stay there at least 20 minutes for proper disinfection.

If for reasons of lack of personnel or time it is necessary to shorten this period, the detergent material should remain for at least 10 to 15 minutes.

5.-  Once the detergent foam has remained for the recommended time, all surfaces including ceiling, walls, incubators and other equipment that can be washed in this way must be washed again. It is important to cover the internal surfaces of the incubators with detergent foam covering 100% of the surfaces including the structures supporting the fans.

Allow the foam to remain on the surface for at least 10 to 15 minutes.

This second wash to remove the detergent should also be done with water under high pressure. If possible, warm water should be used. In this second wash the use of hot water is no longer necessary, unless a significant amount of organic matter is still detected on the surfaces.

6.- In addition to applying high-pressure water at a warm temperature, together with the detergent, it is often necessary and even essential to brush the fans and other structures in order to effectively remove all residues of the incubation process.

“Logically this procedure must be done carefully so that organic matter can be removed without damaging the incubators”

7 Subsequently, the incubators, all equipment and any surface are then thoroughly rinsed. This rinsing should also be done using high pressure water.

The risk of contamination of the chicks’ navel may become worse when they are placed in wet trays

One of the most important aspects to take care of in the hatchery from a sanitary point of view, is cleaning of the chick trays. This is essential as the surfaces of the chick boxes or trays come into direct contact with the navel and skin of the new-born chicks. In each batch there is at least a small percentage of chicks that have been born late and therefore their navel has not yet healed perfectly.

8 After the previous step, all the incubators, equipment and surfaces of the hatchery should  be disinfected with ammonium based disinfectants or an equivalent.

Many hatcheries do not make a final rinse after applying the disinfectant, especially if it is ammonium, since even after drying it has a residual effect that is reactivated when the humidity of the room increases during the incubation process, particularly when the chicks start hatching.

Navels of these chicks can easily become contaminated with bacteria causing omphalitis and infection of the yolk sac. It is impossible to observe the negative effect of this contamination in the hatchery. Instead, that will become clear at three to four during growing when the chicks exhibit increased mortality and when the yolk sac infection and often also the omphalitis is easily observed.

This can become worse when chicks are placed in wet trays, as this further enhances contamination of the navel.

“For this reason, a well-described procedure for washing and disinfecting chick trays should also be in place, as described below”



1 Clearly define the protection procedures for employees in the washing area. It is not just necessary to define these procedures, but also to permanently train all employees, new and old. This training should be done periodically, even for employees who have been working in the hatchery for many years.

2 Thoroughly remove all the fluff, residues of the incubation process and all the organic material from the baskets. Most hatcheries nowadays have automatic washing machines using hot water and detergents. Minimum temperature for washing the baskets should be 70°C.

When not such a system is available, it is critical to wash the baskets manually so that all organic material is removed. When for some reason the chicks have remained too long in the baskets, these will be more difficult to wash and a more rigorous washing procedure than normal will have to be applied.

At the same time, when there is too much blood from the hatching process, that sticks on the baskets, it is also very difficult to clean these. Take into consideration that if salmonella is present, the presence of remaining organic matter on the baskets is an excellent culture for salmonella to multiply.

3 The next step is to apply detergent, if possible at a warm temperature. Allow the detergent to remain on the surfaces of the baskets for at least 15 or 20 minutes. If necessary, brush the baskets manually until all visible organic matter is removed completely. No significant amount of meconium should remain, as it contains a high concentration of bacteria, including salmonella.

4 Rinse the baskets with high pressure water afterwards, as well as the incubators and all equipment

5 Subsequently, disinfectant is applied in the form of ammonium and foam, but also other disinfectants can be applied. It is advisable to rotate disinfectants in the hatchery at least every six months

6 The last step in washing and disinfecting the chick baskets before storage, is allowing them to dry. Many hatcheries do not only have automatic basket washers, but also very efficient dryers. A fundamental rule is to not place chicks in wet baskets, as this is one of the most common reasons for bacterial contamination.

“It should not be forgotten that in addition to baskets, it is very important to wash and disinfect the carts, including wheels.


Many hatcheries share hatching egg carts between farms and between farms and the hatchery. Although this practice is not recommended, it is sometimes unavoidable and in these cases it should at least be ensured that the trolleys and their wheels are thoroughly disinfected to minimise cross-contamination with pathogens such as salmonella.

The best way is to use basket washers that have two tanks, the first to capture most of the organic matter and the second tank for detergent and waste. The temperature of the water should be at least 70 °C in order to degrade the viability of bacteria and to detach organic matter from the baskets.


It is essential to clean and disinfect the ventilation system ducts at least once a week using a disinfectant and a fungus inhibitor. To do so, the evaporation coil must be sprayed, as there is a lot of water condensation in it and therefore the unit tends to enhance fungal growth.

Disposable filters should also be used which can be removed each week and replaced with new filters. This should also be done after each hatch, otherwise significant contamination with fungi such as Aspergillus will occur.


It is important to disinfect the hatchery daily, using a fungus inhibitor. The hatchery should be fumigated immediately after setting new eggs, as well as after transfer.

The hatchery should be treated after transfer and after cleaning at each hatch. Any other compartment, room or cellar in the building should be fumigated once it has been cleaned. The egg storage room should be fumigated only when absolutely necessary, as many disinfectants and fumigants could easily enter through the pores of the eggshell.



Most countries have imposed very strict rules on the use of formaldehyde and even in some countries its use is prohibited. Rather than banning its use, some methodology and equipment should be found to allow for the safe use of formaldehyde in a manner that is not harmful to employees and chicks.

When formaldehyde is used, it should be used for disinfection of hatchers but never for incubators.

A good system has a continuous dosing mechanism with a plunger pump that forces the formaldehyde through closed ducts which lead the formaldehyde to the machines.  In here there is a 100 to 120 cm long part that can absorb up to 12 ounces (350 ml) of formaldehyde every 24 hours.

This dosage will provide a concentration of 30 to 40 parts per million of formaldehyde in each machine, which is the best for inactivating fungi. If the concentration of formaldehyde is too high, it will damage the tracheal epithelium of the chicks even before they hatch.

“Excessive formaldehyde concentrations can increase the mortality rate during the first week”

Excessive concentrations of formaldehyde can increase the mortality rate during the first week and facilitate respiratory problems. When properly used however, it can minimize the mortality during the first seven days of life and increase chick quality.


A valuable tool to evaluate the effectiveness of the washing and disinfection program, is through microbiological laboratory tests. For this purpose, sterile swabs must be obtained from samples from different sites

Obtain samples from the inside of the chick baskets and from the inside of the incubator. Place one McConkey agar plate, one blood agar plate and one Saboureaud culture agar plate into the setter and leave them open for 10 minutes and incubate at 37°C for 48 hours.

Obtain samples from the fan blades inside the incubators, as well as from the HVAC filters and coils. Take samples from the wash tanks and also from the basket washer.

Obtain eggs from the egg storage room and put these on TSA agar. Incubate these samples for 48 hours and examine the plates to determine if the cleaning and disinfection system needs to be improved.

This procedure is recommended to be done inside the hatchery without sending samples to the laboratory, unless there’s a need to determine the genus and species of detected bacteria or fungi.

The idea is to determine if there are variations or deviations from the data considered as normal for the plant. Ask vaccine suppliers or the egg vaccination service company to conduct microbiological audits in the vaccination room and for the egg vaccination or post-vaccination team

Finally, remember that it is useful to have systems to verify the effectiveness of washing, cleaning and disinfection of the hatchery and the incubators


• Kirk Dawkins has worked as a hatchery manager at two major broiler integrators (House of Raeford and Pilgrim’s Pride) in the United States. Currently, Kirk is employed with Jamesway incubators. Also he owns a breeder farm.







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