Small, portable electronic devices need power supplies that have long life, high energy efficiency, high energy density, and can deliver short power bursts. Hybrid power sources that combine a high energy density fuel cell, or an energy scavenging device, with a high power secondary battery are of interest in sensors and wireless devices. However, fuel cells with low self-discharge have low power density and have a poor response to transient loads. A low capacity secondary lithium ion cell can provide short burst power needed in a hybrid fuel cell–battery power supply. This paper describes the polarization, cycling, and self-discharge of commercial lithium ion batteries as they would be used in the small, hybrid power source. The performance of 10 Li-ion variations, including organic electrolytes with Li x V2O5 and Li x Mn2O4 cathodes and LiPON electrolyte with a LiCoO2 cathode was evaluated. Electrochemical characterization shows that the vanadium oxide cathode cells perform better than their manganese oxide counterparts in every category. The vanadium oxide cells also show better cycling performance under shallow discharge conditions than LiPON cells at a given current. However, the LiPON cells show significantly lower energy loss due to polarization and self-discharge losses than the vanadium and manganese cells with organic electrolytes.