There is a concern that the widespread use of antiretroviral drugs to treat HIV infections may result in the increased transmission of a drug-resistant virus. Drug resistance testing before initiating treatment among newly diagnosed HIV patients is helpful in the design of initial regimens. Although HIV infected patients have been increasing in Korea, the transmission rate of drug-resistant HIV is unknown. The aim of this study was to determine the prevalence of antiretroviral drug resistance-associated mutations in patients newly diagnosed as early stage of HIV infection in Korea. We defined patients with early HIV infections as those with confirmed diagnoses who had an indeterminate Western blot. We performed genotypic resistance testing in 66 HIV-1 subjects at an early HIV infection stage who were identified between March 2002 and June 2005. Two of the 66 subjects with early HIV infections showed major mutations associated with resistance. Major mutations by themselves reduce susceptibility to one or more drugs and occur commonly during virological failure. Minor mutations have little or no effect on susceptibility and occur only after other drug-resistance mutations. The resistant mutation of reverse-transcriptase gene was found at E44D, and the major resistant mutation of protease gene was found at M46L. Minor protease resistance mutations were seen in 52 cases. Genetic subtype analysis revealed that all subjects were infected with HIV-1 subtype B. In conclusion, the prevalence of drug-resistant HIV-1 in patients newly diagnosed with HIV in its early infection stage is not high in Korea.