Mitochondria play an essential role in cellular homeostasis. Although in the last few decades our knowledge of mitochondria has increased substantially, the mechanisms involved in the control of mitochondrial biogenesis remain largely unknown. The powerful genetics ofDrosophilacombined with a wealth of available cell and molecular biology techniques, make this organism an excellent system to study mitochondria. In this chapter we will review briefly the opportunities thatDrosophilaoffers as a model system and describe in detail how to purify mitochondria fromDrosophilaand to perform the analysis of developmental gene expression usingin situhybridization.