The Abbott HIVAB and Vironostika HIV-1 Microelisa assays have both been validated for use in the serological testing algorithm for recent HIV seroconversion (STARHS). This ability to identify recently-acquired infection provides valuable insight into the epidemic. The availability of each assay during different periods led to longitudinal studies of annual HIV incidence being based on a mixture of results from each. We investigated whether results from both assays could be reconciled. Using statistical methods, the correlation of the two assays' results and other performance characteristics were examined. Of 378 anti-HIV-1 positive specimens examined by both assays, the Abbott assay flagged 40 as from recent infections, whereas Vironostika flagged 50. The correlation coefficient between screening reactivities in each assay was 0.84, and 0.77 in confirmatory mode. Abbott screening results were significantly higher than its confirmatory results, and some specimens from recent infections may consequently have gone undetected by that assay. This problem was not found with the Vironostika assay. Observational data indicated that the estimated HIV incidence derived from HIVAB results increased as the assay threshold, with its pre-defined seroconversion window, was increased. For Vironostika, the estimated HIV incidence remained stable over a wide range of thresholds. Modelling of the observed relationship between the two assays allowed an estimate of the equivalent threshold in the alternative assay, thus providing a means of reconciling results. Our findings suggest that the Vironostika assay is more reliable than the HIVAB, is easier to use, and is able to allow processing of more specimens per run.