Keeping the Hatchery Clean and Disinfected

By RUI BARROS – Global Incubation Consultant, Petersime NV

The main goal of any hatchery is to produce a maximum number of healthy, uniform day-old chicks, poults or ducklings. Poor hatchery hygiene will lead to increased early embryonic mortality, lower hatchability and more second-grade birds. It is therefore business-critical that hatchery sanitation is taken seriously. This article summarizes step-by-step guidelines on how to effectively clean and disinfect hatchery rooms, incubators and equipment.

General aspects

A hatchery’s biosecurity procedure includes all measures to prevent pathogens from entering the hatchery and reduce the spread of pathogens inside the hatchery. Cleaning and disinfection are an important aspect of proper hatchery biosecurity. Each hatchery room and all hatchery equipment should be properly cleaned and disinfected after each use. Single-stage incubators (‘all-in all-out’) in particular have an important advantage as the allow for frequent quick and thorough cleaning, where as multi-stage incubators are never empty, so they cannot be easily sanitized without interrupting the incubation process.

The seven-step approach to cleaning and disinfecting

Cleaning and disinfection are two separate and distinct procedures in the hatchery sanitation process:

  • Cleaning helps increase the effectiveness of sanitation efforts by removing all debris at a visible surface level. The debris can be a breeding ground for bacteria, fungi and other microorganisms. Therefore, cleaning must always be done first.
  • After ensuring all debris is removed from the room, incubators and equipment, disinfection can be done. Disinfection is what actually eliminates the bacteria, fungi and other micro organisms that may be present in the room and on the machinery.

The two procedures can be performed in sequence or with some time in between, but should always be done in that specific order.


There are four steps in the cleaning protocol that are key to its success:

Step 1

The first step is dry cleaning: Remove all debris from the room, incubators and equipment. It is very important that all surfaces are free from debris. Tools such as brooms, clothes and scrapers are used during this step.

Step 2

After having prepared the surfaces, wet cleaning takes place. Wet cleaning involves applying water with detergent to all surfaces. It is advised to use detergent as it will dissolve impurities and dirt more easily. Why? Cleaning with water and detergent creates foam. The foam formulation will cling to ceilings and vertical surfaces, which is necessary as it actuates the detergent. Foam also makes it visually easier to differentiate soaked and non-soaked surfaces.


  • Use the correct dosage and procedure. If there is too much water or too much pressure, the detergent will splash and not adhere to the surfaces, and therefore lose its effectiveness. If there is too much detergent, the cleaning cost will goup without changing the effectiveness. Using too much detergent also affects waste water treatment.
  • Each detergent requires a specific contact time. Contact time−or ‘wet time’− is how long a detergent must stay on a surface in order to be effective. This time is usually around 20 minutes, but always make sure to check the supplier’s instructions.

Step 3

After this, all surfaces are ready for a thorough rinse with pressure water. Start with the surfaces that are highest up – e.g. ceilings in setters and hatchers– and work down.

Step 4

Remove all remaining water and double-check if all surfaces are thoroughly cleaned. If not, repeat the cleaning protocol steps until all surfaces are perfectly clean.


Always check the user manual of the incubators in your hatchery. Certain setters and hatchers have vulnerable probes and sensors that may require protective covers during cleaning. In Petersime incubators, all probes and sensors are ready to be cleaned straight away.


There are different types of disinfectants available on the market. It is important to match the product to the hatchery environment. If you have to disinfect air ducts, it will be easier to use a gaseous disinfectant. When disinfecting rooms or incubators, a liquid disinfectant will be the best choice.

The disinfection protocol involves three steps:

Step 5

Make sure all cleaned surfaces are dry before applying a disinfectant, since excess water can dilute the disinfectant and affect its performance.

Step 6

Apply the disinfectant as recommended by the supplier. Each product has its own mode of action and requires the correct dosage and contact time.

Step 7

After disinfecting, keep the area sealed to avoid contamination (e.g. by keeping the doors closed).

A good sanitation programme is the cornerstone to preventing pathogens from spreading inside the hatchery.


Cleaning and disinfection protocols are essential to safeguard hatchery biosecurity and produce the highest quality birds. It is the hatchery manager’s responsibility to develop these protocols and schedules for all parts of the hatchery and to take the following important considerations into account:

  • Train staff properly: Hatchery operators must understand the importance of the sanitation work and its impact on the end product’s quality, know the protocols and the different cleaning and disinfection products.
  • Make sure to provide all resources necessary for the staff’s personal safety: protective clothing, goggles and/or masks to protect against skin contact, eye contact and inhalation.
  • Using pressurized hot water is recommended, but be aware that pressure water can potentially affect machine components. Make sure your equipment can take cleaning with high-pressure equipment.
  • Ensure that your choices of detergent and disinfectant used in automated washing machines (e.g. for washing trays and baskets) are appropriate and effective.
  • Make sure to collect debris (e.g. eggshells) in buckets to avoid it goes into the drainage system, possibly clogging the drains.
  • Assess the efficacy of cleaning and disinfection by monitoring the microbial status of the hatchery.

Petersime is happy to help you in learning more about how to run a hatchery with high-level hygiene. The topic is covered in our advanced training programmes, and more particularly the Hatchery Management Training. Please don’t hesitate to contact us for more information.