Periodic health screening of rodents used in research is necessary due to the consequences of unwanted infections. One determinant of the risk of infection for any given agent is its prevalence; other factors being equal, a prevalent agent is more likely than a rare one to be introduced to a research facility and result in infection. As an indicator of contemporary prevalence in laboratory populations of rats and mice, the rate of positive results in the samples received at a major commercial rodent diagnostic laboratory was compiled for this paper. Although samples from laboratory rodent vendors have been excluded, results are tabulated from samples from more than 500,000 mice and 80,000 rats submitted over several years from pharmaceutical, biotechnology, academic, and governmental institutions in North America and Europe, allowing meaningful determination of which agents are common in the research environment versus which agents are rare. In mice, commonly detected infectious agents include mouse norovirus, the parvoviruses, mouse hepatitis virus, rotavirus, Theiler's murine encephalomyelitis virus, Helicobacter spp., Pasteurella pneumotropica, and pinworms. In rats, commonly detected infectious agents include 'rat respiratory virus', the parvoviruses, rat theilovirus, Helicobacter spp., P. pneumotropica, and pinworms. A risk-based allocation of health-monitoring resources should concentrate frequency and/or sample size on these high-risk agents, and monitor less frequently for the remaining, lower-risk, infectious agents.