The risk of contamination by microorganisms, and mostly by Salmonella, is a major concern in the sectors of egg production and egg product manufacturing. Under healthy breeding conditions, the egg content is generally sterile. However, it can be contaminated by a diversified microbiota containing food spoilage microorganisms and sometimes pathogenic bacteria. The egg has however remarkable self-defence properties intended to preserve the embryo of any microbial invasion during its development. This article gives a progress report on the origin of egg contamination and on egg's antimicrobial defence mechanisms. The means to limit the presence and the development of microorganisms in eggs are discussed, at the egg production level, and during egg storage and conditioning. Egg breaking systematically involves the contamination of egg white and egg yolk through contact with the spoiled shells, thus giving rise to highly perishable egg products. The control of their microbiological quality is required, in particular when they are integrated in raw or undercooked food. The means of control are discussed and particularly the respect of good hygiene practices and relevant stabilization processes. The significance of monitoring temperatures for the control of pathogenic and food spoilage microorganisms is particularly underlined.