The technique of indirect calorimetry is now widely used to examine rates of energy production and substrate oxidation in humans. Although the basic principles of indirect calorimetry are well established, it is important to recognize that there are several potential pitfalls in the methodology and data interpretation that must be appreciated to properly understand and apply the results derived from this technique. In particular, one must recognize that the fundamental measurement provided by indirect calorimetry is the net disappearance rate of a substrate regardless of the metabolic interconversions that the substrate may undergo before its disappearance from its metabolic pool. Under most circumstances, direct oxidation represents the major route by which a substrate disappears from its metabolic pool, and the two terms are often used interchangeably. However, under conditions when rates of gluconeogenesis, ketogenesis, or lipogenesis are elevated, the presumed equivalence between oxidation and disappearance may no longer apply, even though the actual measurements derived from indirect calorimetry remain valid. When indirect calorimetry is combined with other in vivo metabolic techniques (e.g., the insulin clamp or radioisotope turnover methods) it can provide a powerful tool for noninvasively examining complex metabolic processes.