Monitoring the health of laboratory rodents is an important tool for improving the quality of animals used in research. However not all animal facilities have the same requirements, and an extensive health screen is not always warranted. Large breeding facilities supplying rodents to multiple institutes are under greater pressure to validate the health status of their colonies than experimental facilities holding rodents for short-term experiments. The biosecurity of the facility and the ability to quarantine and/or rederive imported rodents will impact on the likelihood of a facility remaining pathogen free. The value of performing expensive health screens on rodents in a conventional facility is questionable unless required for disease investigation. There is extensive research about the impact of pathogens on experimental parameters. A review of the type of experimental work being conducted in an animal facility and the common pathogens found in local rodent facilities, can assist in prioritizing the pathogens to be included in health-monitoring. Once the pathogen list is decided, the methodology chosen must take into account factors such as cage type, origin of animals, availability of dependable sentinels, and the value of individual rodents. Technological advances are changing the type of samples required for health monitoring and the number of international laboratories specializing in the health screening of rodents is improving access to health monitoring services. In conducting a cost benefit analysis, the value of utilizing some in-house health monitoring versus outsourcing all work to external laboratories needs to be considered. While the cost of health monitoring provides the boundaries, a good health monitoring programme is designed around the animal facility itself.