The Guide recommends sanitizing cage components, including microisolation cage tops (MCT), at a minimum of every 2 wk. Previously published data demonstrated that mouse MCT microbial loads do not increase until at least 2 wk and that sanitation can be delayed past 2 wk. How microbial loads differ on mouse compared with rat MCT, as well as across different ventilation systems, remains unclear. We hypothesized that MCT microbial loads would be higher in tops from rats compared with mice and would differ according to IVC ventilation system. We evaluated bacterial loads on MCT at serial time points to 90 d from static cages housing mice or rats and from rat and mouse cages on several ventilation systems (mice, 6; rats, 4). MCT were determined to have sufficiently elevated bacterial loads to necessitate changing based on either statistically significant changes in bacterial loads or values greater than 50 cfu. Across all ventilation systems, bacterial counts at 14 d were significantly higher on rat MCT compared with mouse MCT. Across the ventilation systems examined, rat MCT cfu remained similarly elevated from 14 d through 90 d. Mouse MCT total cfu were also stable across multiple ventilation systems yet remained lower than 50 cfu until at least 90 d. Patterns of bacterial species isolated from rat MCT were relatively consistent over time and ventilation system, whereas mice showed greater variability in both contexts. We found that 14 d is an appropriate sanitization time point for rat MCT, whereas the interval at which mouse MCT are cleaned can be extended to 90 d at least. Our data highlight interspecies differences in the accumulation of bacteria on MCT and that mouse MCT sanitation intervals for several housing systems can be extended beyond 14 d.