The microbiological quality of laboratory animals is crucial for the validity and reproducibility of scientific research data, as well as human health and animal welfare. Currently, individual ventilation cages (IVC) have become the mainstream feeding system for rodent laboratory animals. The most commonly used pathogen monitoring method for this feeding system is soiled bedding sentinels (SBS). This method monitors the microbial carrying status of mouse colony through indirect contact and delayed feedback. It can effectively monitor pathogens transmitted via the fecal-oral route, such as mouse hepatitis virus and reovirus. However, this method has difficulty detecting pathogens mainly transmitted through aerosols or direct contact, such as Sendai virus and Pasteurella pneumotropica. The exhaust air dust (EAD)-PCR monitoring method involves swab sampling in the IVC exhaust ducts to monitor the corresponding racks of the ducts; swab sampling before the prefiltration of the host to monitor the entire IVC rack; and EAD collection device sampling to monitor all racks connected to the same host. Different IVC manufacturers have developed corresponding EAD collection devices for their respective IVC systems, making operations convenient and standardization easy. Compared with the SBS method, the EAD-PCR method significantly improves detection rate and timeliness, with the fastest detection possible after one week of exposure. It can serve as a supplement or replacement for the SBS method. Currently, increasing evidence supports that EAD-PCR testing is a more reliable, sensitive, and cost-effective monitoring method, and is more beneficial to animal welfare. This article reviews the application progress of these two methods for monitoring pathogens, analyzes the existing limitations of the EAD-PCR method, and proposes solutions based on its implementation in our laboratory and examination units. The EAD-PCR method helps reduce the number of live sentinel animals used in pathogen monitoring, in order to better maintain the "3Rs" principle of laboratory animal welfare.