Specific pathogen-free (SPF) chickens are widely used in the research of avian diseases and vaccines. Vertically transmissible diseases are transmitted to chickens through vertical transmission, seriously affecting their survival rate, increasing production costs, and causing significant economic losses to the poultry industry, while severely impacting the breeding and use of SPF chickens. Therefore, it is crucial for researchers and managers to enhance their understanding of vertically transmissible pathogens in chickens and to develop effective monitoring measures. Quality monitoring is an important part of ensuring the quality of SPF chickens, with pathogen detection being the primary step. Based on this, it is necessary to cultivate qualified SPF chickens through purification methods and biosecurity measures. This paper reviews the major vertically transmissible pathogens in chickens, including viral pathogens, bacterial pathogens and mycoplasmas, as well as their detection methods. This study compares the differences in microbiological testing items and methods for SPF chickens between the U.S. corporate standard and the Chinese national standard. Analysis of the results shows that in both standards, vertically transmissible pathogens such as Escherichia coli, Proteus mirabilis, Salmonella, and avian leukosis are not included in the microbiological testing items for SPF chickens. Instead, these pathogens are characterized by mixed infections, and outbreaks can seriously affect flock health. To produce higher-quality SPF chickens, it is necessary to include these pathogens in the mandatory testing items. The aim of this paper is to help readers understand the relevant standards for microbiological monitoring of SPF chickens, the hazards of vertically transmissible pathogens, and prevention and control strategies, so as to provide a reference for the detection and purification of pathogens in SPF chickens.