Abstract The flagellated protozoan parasite Trypanosoma brucei is responsible for African trypanosomiasis, which is transmitted by the tsetse fly and causes widespread mortality and morbidity of humans and livestock in sub- Saharan Africa. Sleeping sickness is fatal if untreated, yet no vaccine exists and current treatments are old, toxic and difficult to administer. Thus, there is a pressing need for research to better understand these parasites and facilitate development of new therapeutic interventions. T. brucei depends on its flagellum for cell motility, coordination of signaling in response to the external environment, interaction with host tissues, and cell morphogenesis and division. Thus, the trypanosome flagellum is essential for parasite survival, transmission through the fly vector, and infection of the mammalian host. The long-term goal of our studies is to understand how motility and host-parasite interactions provided by the trypanosome flagellum contribute to infection and pathogenesis. Much is known about flagellum composition and structure, but important questions remain regarding the specific proteins and interactions that underlie trypanosome-specific motility and the role of motility during host infection. To address these knowledge gaps, we will employ motility mutants and mouse infection models to address the role of motility in avoidance of the host immune response and penetration of extravascular tissues, which both impact disease pathogenesis and transmission. We will also use cryoelectron tomography, together with mutational analysis, to build a three-dimensional molecular model of the flagellum and elucidate proteins that comprise trypanosome-specific flagellum structures and functions. Our focus is on the flagellum of T. brucei. However, flagella are important for many other pathogenic protozoa as well as for normal human development and health. Therefore, we expect our results to be of wide interest for the community studying pathogenesis of parasitic protozoa, human development and physiology, and fundamental biology of eukaryotes.