The health of laboratory animals is vital to their suitability for research. Therefore, an animal health quality control program is important to any research facility. This guidebook concentrates on infection surveillance for rodent populations, provides a brief overview of agents to consider as part of a program and offers recommendations for the selection of assays, sample type and number and testing frequency. It also incorporates recent advances that can reduce or eliminate the need to use animals as sentinels. Although we focus on the theory behind creating a modern infection surveillance program, we also briefly discuss the response to microbial outbreaks and a few basic aspects of biosecurity. The recommendations in this document are based on information from current texts, relevant scientific literature and actual experience working with both Charles River rodent production facilities and customer vivaria.