Background: Drug warehouse at health centres is one of pharmacy service that should be paid attention to store medication and ensure the quality. The study aimed to analyze the availability and eligibility of drug warehouse at health centres in Indonesia based on geographic location and topography of the health centers. Methods:It is a further analysis on secondary data from Health Facility Research year 2011 which conducted in 33 provinces of Indonesia. Results: There were more than 90% of health centres available drug warehouses in Indonesia based on the geography and topography conditions, except in very remote area just 89.7%. The highest component of warehouse facilities on reporting and drugs storage facilities were logistick and distribution in 2010, meanwhile the lowest was supporting facilities as narcotics/psychotropic cabinet. The availability of that facilities is lower in remote, borderline and islands area. The eligibility of warehouse at health centers in Indonesia showed the majority were classified as eligible but in the remote, bordeline and islands areas are lower. The statistical analysis (Mann Whitney and Spearman correlation) were significant associations between eligibility warehouse by geographic and topographic of island and remote areas. Conclusion: The availability and eligibility of warehouse at health center in Indonesia the majority were classified as eligible but in the remote, bordeline and islands areas are lower. Recommendation: Central and local governments should assure increase facilities and infrastructure of drug warehouses by increasing health budget to ensure appropriate and standardized drug storages.