A patient who presented with late stage HIV-associated diseases could not be diagnosed by commercial ELISA tests and a Western blot. However, we could amplify proviral DNA of HIV-1. We found a novel GPGGMI motif in the V3 loop, a novel insertion of a proline in the C3 region, and persistent deletion of two amino acids in the vif gene. The patient had been treated with HAART after diagnosis. Forty months after the first amplification of HIV-1 DNA, anti-HIV-1 antibody was confirmed by ELISA and Western blot and, thus, we amplified and sequenced HIV-1 full sequences. Interestingly, the sequence at the TATAA box was TAAAA, although full sequences were not CRF01_AE. The major differences in the level of the HIV-1 gene between the seronegative and seropositive states were changes at the glycosylation site (NXT) next to the inserted proline and many resistance mutations including M184V to antiretroviral drugs occurred. This is the first report on HIV-1 full sequences isolated from seronegative AIDS patients infected with subtype B in Korea.