Nine isolates of HIV-1 obtained from Congolese AIDS patients were amplified by the polymerase chain reaction (PCR) using primer pairs and oligomer probes derived from the HIV-1 LAV-BRU (BRU) sequence. When compared to BRU, two isolates exhibited a significant decrease of PCR efficiency with a given primer pair. Moreover, the DNA amplified from two other isolates did not hybridize with the corresponding probe despite efficient PCR. Base substitutions were detected in the regions of proviral genomes involved in oligonucleotide annealing and were assumed to be responsible for the failure of both amplification and probing. Our data confirm that the genetic variability of HIV-1 may reduce the efficiency of PCR as a diagnostic procedure, especially in the case of African isolates.