As illustrated elsewhere in this volume, Tetrahymena is an extraordinary experimental system in which molecular genetics, biochemistry, and cytology can be applied to the study of a cell biological problem. Our long-term goal is to understand how the different structural domains of dynein contribute to its function. Our strategy is to create targeted modifications in an axonemal dynein heavy chain gene, recover the dynein protein from cilia, and evaluate the in vitro activity of the isolated dynein. In this chapter, we have summarized our procedures for the isolation and characterization of the ciliary outer arm dynein.