Chemical composition, physical characteristics and structural features of a natural FeS2 powder and a synthetic FeS2 sample were correlated with their specific discharge capacities in lithium cells. The levels of impurity elements, primarily present as second-phase oxides and sulfides, were significantly higher in the natural FeS2 than in the synthetic sample. These impure second-phases were electrochemically inactive, and they did not have any significant effects on the discharge of Li/FeS2 cells. Trace amounts of impurity elements were detected in solid solution of FeS2 pyrite and the pyrite structure was nearly ideal for both the natural and synthetic samples. A sulfur-deficient pyrrhotite FeS1.3 phase was found in the center of some large synthetic FeS2 particles, which was electrochemically active at 1.5 V versus lithium. Optical microscopy showed that the grain sizes within synthetic FeS2 particles were significantly smaller than those within natural FeS2 particles. The superior rate capability of Li/synthetic FeS2 cells was attributed primarily to the smaller grain sizes within synthetic FeS2 particles in comparison to the natural FeS2 sample.