The system of Rodent health monitoring is critically and crucially dependent upon diagnostics. There are two most important reasons to keep research rodents healthy and free from infections those are; to protect the health and welfare of research rodents and detection and subsequent elimination of disease factors at early stages by using ideal methods can prevent infections from negatively impacting research. Sub clinical infections in rodents modify or alteration in research outcome. In India, over and above 1500 facilities are using laboratory animals for biomedical research. However, majority of them have not implemented the comprehensive disease diagnostic programme or health monitoring due to prohibitive cost of the diagnostic kits. Few facilities in India have implemented international guidelines in health monitoring/disease diagnosis and this includes conventional methods, ELISA and PCR for rapid diagnosis. The expansion of various molecular techniques has developed diagnostic procedures by providing specific diagnosis or detailed characterization of any pathogen or host pathogen interactions. Some of the current immunological and molecular techniques in addition to the conventional ones for the diagnostic technique are discussed in brief. These techniques have been advanced and recognized elsewhere needs to be implemented for rapid and accurate diagnosis of rodent pathogens.