The use of high activity antiretroviral therapies (HAART) to treat HIV-infected patients frequently results in the long-term suppression of plasma virus RNA loads below levels detectable by current assays. The measurement of provirus DNA load in peripheral blood mononuclear cells provides a means of continuing to monitor the efficacy of treatment and the decline in reservoirs of latent virus. A quantitative PCR assay was developed for HIV-1 provirus using a three-point internal calibrator system to give high reproducibility and accuracy at the low copy numbers of provirus seen in clinical samples. Provirus DNA copies are related to cell number in the samples using a fluorescent dye-binding assay for measurement of input DNA. The assay agreed closely with an end-point dilution PCR and gave accurate quantification of extracts from an HIV-1 infected continuous cell line containing known provirus copy numbers. The inclusion of a second primer set in the LTR region of the HIV-1 genome, optimised to non-clade-B virus strains improved the detection and quantification of samples from patients infected with genetically divergent virus strains. Application of the assay to clinical trial patients showed no relationship between changes in provirus DNA loads and plasma virus RNA and changes in provirus load over 24 weeks were small.