Background: Establishment of Early Warning Alert and Response System (EWARS) in Indonesia was initiated since 2009 in few selected provinces and government was planning to roll out in other provinces. Before initiating this roll out the assessment of performance of EWARS in 2012 was conducted. The aim of the assessment is to strengthen laboratory for supporting to EWARS for alerts testing. Methods: Laboratory capacity mapping tool and laboratory algorithm for twenty two priority diseases of EWARS were developed. This mapping tool was used in nine provinces to look at the existing capacities. This mapping tool and algorithm is used to pilot the laboratory support function for EWARS in four districts of West Kalimantan. Results: Almost all alerts have no laboratory confirmation except for few disease like measles, poliomyelitis and malaria. Capacity mapping of five of the nine provinces have available capacity for testing for bacteriology, virology, parasitology, mycology, hematology, immunology and environmental/chemicals in public or private sectors. A piloting of laboratory support for EWARS demonstrated the application of algorithm, development of logistic planning and allocation of resources for laboratory testing for alerts of EWARS. Conclusion: Capacity mapping opens horizon on strengthening support function of the system, which are readily available at local levels and provides opportunities for coordination and collaboration. EWARS is an opportunity to strengthen sustainable and sensitive surveillance system, which in turn assist on overall of health development through health systems strengthening.