In this work, we report on the applicability of two-dimensional high-performance liquid chromatography (2D-HPLC) for the comprehensive characterization of inactivated influenza vaccine proteins. This novel procedure features minimal sample treatment and combines the on-line coupling of size exclusion HPLC to reversed-phase HPLC. A comparative analysis of commercial vaccines from three different manufacturers showed the method to be highly selective by providing characteristic reproducible chromatographic profiles for each vaccine. In addition, the method provided enhanced sensitivity for most constituents as a result of the use of native fluorescence detection in the reversed-phase HPLC step. The limits of detection (at a signal-to-noise ratio of >3) for hemagglutinin (HA) antigens were 105 and 172 ng/mL for influenza A/New Caledonia/20/99 and B/Jiangsu/10/2003 strains, respectively. The potential of this 2D-HPLC procedure in terms of quantitative antigen analysis was assessed by determination of the HA content of commercial vaccines. Results provided very good correlation with nominal HA values. The reproducibility (RSD) of the whole procedure was also evaluated and was found to be better than 2 and 3% for calculated antigen concentrations expressed as micrograms of HA per milliliter in commercial vaccines for samples of the same lot (n = 5) or different lots (n = 3), respectively. In addition, it allowed the selective detection of several influenza constituents including nucleoproteins from type A and B viruses and the highly hydrophobic matrix protein 1 from both virus strains.