Tsetse flies (Diptera: Glossinidae) are vectors of several species of pathogenic trypanosomes in tropical Africa. Human African trypanosomiasis (HAT) is a zoonosis caused by Trypanosoma brucei rhodesiense in East Africa and T. b. gambiense in West and Central Africa. About 100000 new cases are reported per year, with many more probably remaining undetected. Sixty million people living in 36 countries are at risk of infection. Recently, T. b. gambiense trypanosomiasis has emerged as a major public health problem in Central Africa, especially in the Democratic Republic of Congo, Angola and southern Sudan where civil war has hampered control efforts. African trypanosomes also cause nagana in livestock. T. vivax and T. congolense are major pathogens of cattle and other ruminants, while T. simiae causes high mortality in domestic pigs; T. brucei affects all livestock, with particularly severe effects in equines and dogs. Central to the control of these diseases is control of the tsetse vector, which should be very effective since trypanosomes rely on this single insect for transmission. However, the area infested by tsetse has increased in the past century. Recent advances in molecular technologies and their application to insects have revolutionized the field of vector biology, and there is hope that such new approaches may form the basis for future tsetse control strategies. This article reviews the known biology of trypanosome development in the fly in the context of the physiology of the digestive system and interactions of the immune defences and symbiotic flora.