Use of soiled bedding sentinels (SBS) for rodent colony health monitoring is limited by inconsistent pathogen detection, reliance on live animals, high costs, and labor intensity. Sentinel-free soiled bedding (SFSB) offers a viable alternative for all rodent housing systems, overcoming limitations by using PCR testing of matrices exposed to soiled bedding. As an alternative, a matrix may be exposed to all cages via direct colony dredging (DCD). This study compared pathogen detection and costs between SFSB, DCD, and SBS for mice housed in individually-ventilated cage rack system cages. For each study rack, SFSB was performed with one matrix shaken in composite soiled bedding, while DCD was performed with a second matrix exposed to all soiled cages on the rack using a dredging method. We hypothesized that the SFSB and DCD matrices would detect Rodentibacter heylii, Rodentibacter pneumotropicus, Helicobacter typhlonius, Helicobacter mastomyrinus, Helicobacter hepaticus, Helicobacter bilis, Helicobacter rodentium, Helicobacter ganmani, and murine norovirus (MNV) with equal or superior efficacy to SBS, at a comparable or reduced program cost. All SBS failed to detect R. heylii, R. pneumotropicus, H. typhlonius, H. mastomyrinus, H. hepaticus, H. bilis, H. rodentium, and H. ganmani when tested by fecal PCR, and 25% failed to detect MNV when tested via serology. In contrast, SFSB and DCD matrices detected MNV, R. heylii, R. pneumotropicus, H. typhlonius, H. mastomyrinus, H. hepaticus, H. bilis, H. rodentium, and H. ganmani even with low pathogen prevalence, although neither method achieved 100% detection. DCD had negative ergonomic, workflow, and labor challenges compared with SFSB. Overall, SFSB and DCD had reduced costs and superior pathogen detection compared with SBS, while SFSB provided the most efficient and user-friendly approach for health monitoring by this institution.