Mitochondrial dysfunction has gained a preponderant role in the pathogenesis of Huntington's disease (HD). Mutant huntingtin (mHTT) directly interacts with mitochondria in a deleterious manner. As the central hub of the cell, not only mitochondrial bioenergetics is affected but there is also diminished mitochondrial membrane potential (Δψ ) and altered production of reactive oxygen species (ROS). Restoration of mitochondrial function has proven to be a major player in the search and establishment of therapeutics for HD patients. As such, performing an overall study of mitochondrial function is crucial. In this chapter, we describe some methodologies used to study mitochondrial function by determining the oxygen consumption, changes in Δψ, mitochondrial calcium handling, and levels of mitochondrial ROS. Here we focus on biological samples derived from HD versus control cells and/or animal models, namely functional isolated brain mitochondria, an ex vivo animal model, and cultured cells, including cell lines and primary neural cultures, as in vitro models.