HIV infection is one of the major threats to human health due to the lack of relevant vaccine and drugs to cure AIDS. Its early diagnosis is thus important in controlling HIV transmission. Molecular diagnosis of HIV can be performed qualitatively and quantitatively. Currently, molecular diagnosis of HIV infection is only used as a complementary diagnosis although viral load test is used to monitor disease progression and responsiveness to antiviral therapy. To optimize HIV assays, a variety of technological advances, such as the introduction of dUTP/UNG system, real-time detection platform, and coupling of more than one enzyme in molecular identification, have been integrated into new methods. With the development of more reliable HIV assays in the future, the molecular diagnosis of HIV is expected to be accepted as one of the standards in determining whether there is a HIV infection in resource-rich laboratories, which will play a crucial role in reducing HIV transmission.