Eastern Africa was probably the first region to which HIV was carried from its western equatorial origin, along several different routes that cannot now be traced in detail. The virus entered a region divided historically into two contrasting natural and social environments: the well-watered, densely peopled kingdoms around Lake Victoria and on the Ethiopian plateau, and the less centralised societies in the drier savanna country where population clustered only on highland outcrops, in colonial cities along transport routes, and on the Indian Ocean coast. This framework gave HIV/Aids in eastern Africa its distinctive contrast between explosive epidemics in the Lake Victoria basin and the capital cities, on the one hand, and slow penetration into the remainder of the region, on the other. Varying relationships between cities and countryside were especially important in the process, as were the mobile groups linking them together and the factors - widespread labour migration, male predominance in urban populations, low status of women, lack of circumcision, and prevalence of sexually transmitted diseases - that bred higher levels of infection than in western equatorial Africa.

The virus first entered the Lake Victoria basin bordering the DR Congo. Patients from Rwanda and Burundi were seen alongside Congolese in European hospitals during the late 1970s and early 1980s. They not only led expatriate researchers to visit Kigali as well as Kinshasa in 1983 but encouraged observers of the epidemic to believe that Rwanda, Burundi, and perhaps even Uganda had been simultaneous or even earlier places of origin alongside western equatorial Africa. The location of the chimpanzee host makes this unlikely, however, as does the distribution of HIV-1 subtypes, for there is no indication in the Lake Victoria basin of the diversity of strains found in the DR Congo. Until well into the epidemic, the A and D subtypes dominated the region.

In Rwanda the first probable case recorded was a mother who displayed characteristic opportunistic infections in 1977 and subsequently tested positive for HIV along with her husband and three children. A retrospective study found that by 1982 some 12 per cent of blood donors in Kigali were infected.