Conservation translocations carry an inherent disease risk. Rodent translocations are arguably of particular risk as their life-history traits make them ideal disease reservoirs. However, currently there is a poor understanding of the baseline health of Australian rodents, especially for species inhabiting semi-arid and arid environments where assumptions of equivalence with mesic counterparts are inappropriate. Although deficiencies in baseline knowledge pose challenges for wildlife disease risk analyses (WDRA), the WDRA process can provide an opportunity to identify how translocations and attached ecological monitoring programs may begin to address these knowledge gaps. Early planning and collaboration enabled the implementation of recommendations from the Dirk Hartog Island rodent translocation WDRA. A three-year project involving targeted and passive disease surveillance of source and recipient rodent populations was established. We focussed on both translocated and extant rodents to ascertain baseline health data prior to and during translocation. Through this project we have increased our understanding of pathogen diversity and possible health implications in semi-arid and arid-zone murids. Our results emphasise the need for ongoing island biosecurity and hygiene vigilance for both wildlife and human health, and identified non-infectious hazards that may require more intensive risk mitigation. Several challenges were encountered, including species size, absence of validated diagnostic tests, and logistical challenges. However, the project has demonstrated the value of incorporating WDRAs and allocating resources to health and disease monitoring to maximise the knowledge gained from translocation programs.