Li batteries, including secondary and cylindrical/button primary Li batteries, are used worldwide in computers, communications and consumer electronics products. However, there are several dangerous issues that occur during the manufacture, shipping, and storage of Li batteries. This study analyzes the material flow of lithium batteries and their valuable heavy metals in Taiwan for the year 2006 by material flow analysis. According to data from the Taiwan Environmental Protection Administration, Taiwan External Trade Development Council, Bureau of Foreign Trade, Directorate General of Customs, and the Li batteries manufactures/importers/exporters. It was found that 2,952,696 kg of Li batteries was input into Taiwan for the year 2006, including 2,256,501 kg of imported Li batteries and 696,195 kg of stock Li batteries in 2005. In addition, 1,113,867 and 572,215 kg of Li batteries was domestically produced and sold abroad, revealing that 3,494,348 kg of different types of Li batteries was sold in Taiwan. Of these domestically sold batteries, 504,663 and 146,557 kg were treated domestically and abroad. Thus, a total of 2,843,128 kg of Li batteries was stored by individual/industry users or illegally disposed. In addition, it was also observed that 2,120,682 kg of heavy metals contained in Li batteries, including Ni, Co, Al, Cu and Ni, was accumulated in Taiwan, with a recycled value of 38.8 million USD. These results suggest that these heavy metals should be recovered by suitable collection, recycling and reuse procedures.