Eggs can be fumigated during incubation or at pipping (during or just after the transfer to the hatcher), but most commonly prior to incubation. Formaldehyde, besides being an excellent anti-microbial agent, is also a toxic chemical and, as such, can seriously damage the dormant embryo if fumigation is carried out improperly. The part of the egg most exposed to the fumigant is the outmost organic layer, the cuticle, an important barrier to microbial invasion. Any damage of the cuticle may have serious consequences during incubation. The aim of fumigation is therefore twofold: to reduce microbial count and to minimise the adverse effects of contamination whilst causing as little damage to the developing embryo as possible. In order to fumigate effectively, the balance must be found.

Formaldehyde (H2CO, formalin, formol) is a gas at room temperature and it is readily soluble in water. It is commonly used as a disinfectant, as it is cheap, not corrosive, and kills most bacteria and fungi (including their spores). The biocidal efficacy of formaldehyde is due to its ability to act on the proteins and nucleic acid bases of microorganisms  By attaching itself to the primary amide and amino groups of proteins, formaldehyde forms stable methylene bridges and, hence, intermolecular cross-linkages. In addition, formaldehyde also alkylates the nitrogen atoms of purine and pirimidine bases in DNA and RNA.

Formaldehyde may be applied as a liquid but it is more effective when used as a gas. The gas can be generated by several methods, but the most common way used in the poultry industry was the addition of formalin to potassium permanganate (KMnO4) in 2:1 ratio (v/w). This is now being superseded by the volatilisation of the polymer paraformaldehyde under controlled temperature.