The development of the purification process for VAQTA, which results in a highly purified inactivated hepatitis A vaccine, was driven by modifications in the cell-culture and harvest methods which permit hepatitis A virus propagation to support large-scale manufacture. The starting material for the purification was initially a concentrated cell pellet scraped from roller bottles. However, when the cell-culture method was scaled up to use high-surface-area Nunc cell factories or Costar cubes, the early steps in the process had to be modified to handle large volumes of dilute lysate. Membrane concentration was used at first, and a highly purified vaccine was prepared, but virus-poly(nucleic acid) complexes were formed, which reduced the yields in later processing steps. The introduction of a nuclease digestion immediately after harvest followed by capture chromatography on an anion-exchange column eliminated the formation of these complexes and resulted in more consistent performance and higher yields of downstream operations.