The third type of test is a PCR test (Polymerase Chain Reaction test). The whole process of extracting genetic material and testing it with a PCR test is referred to as Nucleic Acid-amplification Testing or 'NAT'. PCR tests detect the genetic material of HIV itself, and can identify HIV in the blood within two or three weeks of infection.

PCR tests come in two forms: DNA PCR and RNA PCR. Babies born to HIV positive mothers are usually tested using a DNA PCR because they retain their mother's antibodies for several months, making an antibody test inaccurate. Blood supplies in most developed countries are screened for HIV using an RNA PCR test, which can produce positive results several days before a DNA test. When a person already knows that she or he is infected with HIV, they may also have a viral load test to detect HIV genetic material and estimate the level of virus in the blood. This can be performed using either an RNA or DNA PCR test. PCR tests are not often used to test for HIV in adults, as they are very expensive and more complicated to administer than a standard antibody or P24 test. However they may be offered in special circumstances, or by private clinics where patients are willing to pay.

Blood supplies in most developed countries are screened for HIV using an RNA PCR test, which can produce positive results several days before a DNA test.