Interest in recycling of rare metals has greatly increased recently because of the rapid growth in the demand for, and uneven distribution of, natural resources. Substance flow analysis (SFA) is a useful tool for determining the flow of substances in specific geographic regions. However, few SFAs have been conducted for rare metals. In this paper, we focus on indium and conduct SFAs of indium both in Japan and globally. Indium is primarily used as indium tin oxide (ITO), whose end uses can be categorized into two groups: liquid crystal displays and plasma panel displays; these are then assembled into final products. We quantified the flow of indium during its life cycle through mining, smelting and refining, manufacturing, use and waste management. For mining, smelting and refining, data were collected on the indium content in ore and production of primary metallic indium during 1999–2008. For manufacturing, we estimated the content of indium in final products, and estimated the input of indium in production as ITO in Japan. Then, we extrapolated the result to an SFA at the global scale. In-use stock and discarded indium were estimated by dynamic SFA, in which time-series data on the input of indium into final products and their lifetime distribution were used. We considered the loss of indium in each process to be the potential recyclable amount. We found that the extraction rate of indium in the mining, smelting and refining process was 8–11%, and the loss of indium in this process was 4,826 t in 2004. The loss in manufacturing amounted to 316 t, the in-use stock of indium was 116 t and the discarded indium in end-use products amounted to 5 t globally in 2004. Therefore, it was concluded that the biggest recovery potential of indium is during mining, smelting and refining.