The bacterial and viral load of an egg must be as little as possible when eggs are entering the incubation process. Bacterial and viral contamination at this point can lead to excessive spreads.

Egg disinfection helps to reduce the bacterial and viral load. It is important that especially at the start of the incubation process the eggs are as clean as possible, and disinfection at this point is highly recommended!

Other moments when disinfection can be done:
- At the farm, directly after collection
- During transportation from farm to hatchery
- Upon arrival at the hatchery
- Just before setting (this is the most important moment)
- After transfer
- At hatch

In addition to this, a continuous light disinfection in the machines can be given. Especially in multi-stage machines, this is practiced as they can not be cleaned sufficiently between batches.

Methods for disinfection include:
- Fumigation (e.g. formaldehyde)
- Spraying (e.g. hydrogen peroxyde, quaternary ammonium, etc.)
- UV radiation
- Use of Ozone

In principle, method such as Gamma radiation can also be used, but this is not practically applicable at this moment.