HIV-1 integration is an essential step in the virus replication cycle leading to establishment of virus persistence in infected patients. We have developed an Alu-PCR assay to specifically measure integrated viral DNA levels in HIV-1 infected cells [1, 2]. The assay makes use of a primer complementary to Alu repeat elements in the cell chromosome and another specific for the PBS region of the HIV-1 genome. This integration specific and sensitive assay has been adapted to the more rapid and quantitative real-time PCR format. We describe two critical applications of this assay – firstly for the measurement of integrated viral DNA load (iVL) in patient samples, and secondly for assessing the specific anti-HIV-1 integration activity of semi-purified preparations from the root of Salvia miltiorrhiza (Danshen) in HIV-1 acutely infected T cells. Results showed that quantitative iVL measurements could be determined in PBMCs isolated from fresh blood samples using this assay and that iVL did not necessarily correlate with plasma viral load in the same sample. Use of the Alu-PCR assay in preliminary analysis of Danshen root extracts indicated that all compounds that were tested exhibited inhibitory activity upon HIV-1 reverse transcription and integration.