INTRODUCTION: The mass rapid transit (MRT) is the largest transport infrastructure project under the national key economic area (NKEA) in Malaysia. As urban rail is anticipated to be the future spine of public transport network in the Greater Kuala Lumpur city, it is important to mainstream climate change mitigation and public health benefits in the local transport development. This study quantifies the health co-benefits in terms of mortality among the urbanites when the first line of the 150 km MRT system in Kuala Lumpur commences by 2017. METHOD: Using comparative health risk assessment, we estimated the potential health co-benefits from the establishment of the MRT system. We estimated the reduced CO2 emissions and air pollution (PM2.5) exposure reduction among the general population from the reduced use of motorized vehicles. Mortality avoided from traffic incidents involving motorcycles and passenger cars, and from increased physical activity from walking while using the MRT system was also estimated. RESULTS: A total of 363,130 tonnes of CO2 emissions could be reduced annually from the modal shift from cars and motorcycles to the MRT system. Atmospheric PM2.5 concentration could be reduced 0.61 μg/m3 annually (2%). This could avoid a total of 12 deaths, mostly from cardio-respiratory diseases among the city residents. For traffic injuries, 37 deaths could be avoided annually from motorcycle and passenger cars accidents especially among the younger age categories (aged 15-30). One additional death was attributed to pedestrian walking. The additional daily physical activity to access the MRT system could avoid 21 deaths among its riders. Most of the mortality avoided comes from cardiovascular diseases. Overall, a total of 70 deaths could be avoided annually among both the general population and the MRT users in the city. CONCLUSION: The implementation of the MRT system in Greater Kuala Lumpur could bring substantial health co-benefits to both the general population and the MRT users mainly from the avoidance of mortality from traffic injuries.