Introduction: Human Immunodeficiency Virus-1 (HIV-1) is the most common infection of an unresolved global disease that has had massive impact on human life since its emergence. Transmission of HIV-1 is still rapidly spreading despite identification over 33 years ago and an immense worldwide research effort to counter it. Objectives: The aim of this study is to determine the HIV-1genotype and subtypes that cause AIDS in Sudan. Methods: Samples were investigated and analyzed in three different laboratories; two in Sudan and the third one in Kenya, the Central Lab of Omdurman Military Hospital, Department of Microbiology, Virology Lab of Faculty of Medicine University of Khartoum and Kenya Medical Research Institute (KMERI) -Virus Research Center- Nairobi Kenya. Results: HIV-1 was detected by RT-PCR at the virology lab and the result revealed (188) samples (90.9 %) positive for HIV- 1 (12) samples (9.1%) were negative for HIV-1. Concerning HIV-1 subtypes or clades one hundred of EDTA samples were processed at Kenya Medical Research Institute (KMERI), Using hetero-duplex Mobility Assay Technique (HMA) for env gene. Three subtypes were detected: subtype (A) (46%), Subtype (C) (33%) and subtype (D) (21%). CD4 count was estimated before antiretroviral therapy and three month after treatment, it was found that 71% were responding and 29% were not. Conclusion: The study concluded that the detected HIV subtypes in Sudan were subtypes (A) (C) and (D). Most of the patients were responding to ARV.