Polymerase chain reaction (PCR) was used to amplify a long sequence of human immunodeficiency virus (HIV) DNA, to assess the correlation between PCR signal and clinical stage of disease, and to demonstrate the genotypic variability of different HIV isolates. Twenty-four (96%) of 25 anti-HIV-reactive patients and none of 12 controls were positive for HIV proviral DNA by PCR. After quantification of the PCR signal, a significant difference in the relative amount of HIV proviral DNA per 10(5) peripheral blood mononuclear cells between symptomatic patients (Centers for Disease Control [CDC] class IV) (32,284 +/- 5225 cpm [mean +/- SE], equivalent to 802 HIV plasmid DNA copies) and patients without symptoms (CDC class II/III) (5484 +/- 1469 cpm [mean +/- SE], equivalent to 67 HIV plasmid DNA copies) was observed (P less than .01). Restriction analysis of PCR products in selected samples showed extensive genetic polymorphism between different isolates and more than one viral genotype per isolate. There was a clear correlation between the appearance of clinical symptoms in HIV infection and high levels of viral replication.