HIV is primarily a sexually transmitted disease, but little is known about the transmission of viral variants during sexual contact. An understanding of the types of viruses transmitted by sex may make it possible to design vaccines to prevent the transmission of HIV. In this study we used the rhesus macaque/SIV model to test the hypothesis that a limited number of variants are transmitted during vaginal inoculation with SIV. Five animals were inoculated IV with SIVmac251 and 5 animals were inoculated intravaginally (IVAG) with the same virus stock. The virus loads were assessed using RT-QC-PCR and the number of viral RNA variants in the plasma of the animals was assessed using a heteroduplex mobility assay. The IV inoculated animals had higher virus loads and a higher number of virus variants than the IVAG inoculated animals. In addition, the IV inoculated animals had a more rapid clinical course than the IVAG inoculated animals. This is the first demonstration that a limited number of variants in an SIV stock are capable of initiating a systemic infection after IVAG inoculation. *KEY*Mucosal adjuvants, HIV mucosal immunity, SIV antigens