BACKGROUND: Among patients infected with hepatitis B virus (HBV), quantification of hepatitis B e antigen (HBeAg) is accruing substantial clinical relevance as a marker for HBeAg-loss during treatment. No direct comparison has been made between assays that quantify HBeAg. OBJECTIVES: To compare the performance of HBeAg quantification (qHBeAg) between Architect and Elecsys HBeAg assays among 183 patients with chronic HBV infection (94 treatment-naïve HBV-monoinfected and 89 antiretroviral-experienced HIV-HBV co-infected). STUDY DESIGN: qHBeAg was determined in Paul Erlich Institute Units (PEIU)/mL using previously designed protocols. Values were compared with correlation and linear regression. Bland-Altman analysis was used to compare mean differences (d¯) between Elecsys and Architect assays and limits of agreement (LOA) (±2 standard deviations [SD]). RESULTS: Between-assay correlation was significant overall (r=0.970), yet stronger for qHBeAg<1000 (n=131) versus >1000PEIU/mL (n=52) as determined by the Elecsys assay (r=0.969 vs. 0.880, respectively). On average, the Elecsys assay reported qHBeAg at 13.3PEIU/mL lower than the Architect assay (LOA: -415.9, 389.3), while LOA between assays were much wider at higher levels (<1000: -198.2, 147.9; ≥1000PEIU/mL: -688.4, 721.5). Further analysis indicated that d¯ did not change substantially with respect to HBV genotype, precore mutation, and CD4+ cell count, regardless of HBeAg-level. Nevertheless, seven of eight patients with highly divergent between-assay results had HBV-DNA>2000IU/mL. CONCLUSIONS: Elecsys and Architect assays report similar qHBeAg units with high correlation. Since qHBeAg was performed using an in-house approach, a commercially-available assay could reduce between-assay discrepancies, especially at higher HBeAg-levels.