Rechargeable Li-containing batteries are a promising technology for efficient energy storage.  However, significant challenges need to be addressed before they could be deployed to large-scale system applications in plug-in electric vehicles, renewable energy management, and the power grid. We have carried out critical in situ neutron measurements on Li distribution and transport during the battery operation, and gain new insights in the function and failure of battery systems.  Four neutron measurement techniques, neutron depth profiling (NDP), neutron reflectivity (NR), small angle neutron scattering (SANS), and neutron imaging (NI) have been used to quantify real-time information of the Li transport in electrode, sub-nanometer interfacial structures, and fracturing of electrode particles.  Using examples, we demonstrate that in situ neutron diagnoses offer new opportunities in better understanding the performance and lifetime of secondary batteries.