The genetic subtypes of HIV-1 in the Sudan epidemic have not been characterized. Here we report the partial sequencing and analysis of 30 strains collected from HIV-1-positive patients and blood donors in Khartoum in 1998 and 1999. From analysis of partial pol and env sequences, it was determined that 50% were subtype D and 30% were subtype C. Of interest, some subtype D clustered with those from East Africa whereas others joined subtype D from West Africa. Subtype A, subtype B, and three unique recombinants were also found, some partially unclassifiable. One unclassified strain matched another reported previously from the Democratic Republic of Congo. Sudan borders nine other African countries, and has suffered more than 20 years of civil strife with large population displacements. The intermixing of HIV-1 subtypes previously separated in Africa may be occurring there, with the potential to generate novel new strains by recombination.