On 16 January 2013, all Boeing 787 Dreamliners were indefinitely grounded due to lithium-ion battery failures that had occurred in two planes. Subsequent investigations into the battery failures released through the National Transportation Safety Board (NTSB) factual report, the March 15th Boeing press conference in Japan, and the NTSB hearings in Washington D.C., never identified the root causes of the failures—a major concern for ensuring safety and meeting reliability expectations. This paper discusses the challenges to lithium-ion battery qualification, reliability assessment, and safety in light of the Boeing 787 battery failures. New assessment methods and control techniques that can improve battery reliability and safety in avionic systems are then presented.