A segmented genome enables influenza virus to undergo reassortment of viral RNP complexes when two viruses replicate within the same cell. Reassorted progeny have gene constellations comprising RNPs from both parents which may provide them with novel phenotypes. This process is a major contributor to the emergence of novel pandemic strain but despite its significance, the factors that govern gene selection during reassortment are not understood. We have studied reassortment in its practical context when used to produce viruses carrying gene constellations that improve yields of haemagglutinin (HA) for influenza vaccine production. Using methodology equivalent to seasonal influenza vaccine seed production, we co-infected eggs with A/Udorn/302/72 (Udorn) virus as a model seasonal strain and the high HA-yielding A/Puerto Rico/8/34 (PR8) virus and isolated the progeny under selective pressure of antibody to PR8 surface glycoproteins. In the initial stages a large variety of viruses were isolated but with subsequent rounds of passaging, specific gene constellations came to dominate. After limit dilution, many of the dominant reassortants expressing high levels of HA activity also showed enhanced growth. However a few had poor growth. Our data are consistent with the notion that preferential packaging of certain gene segments with the Udorn surface glycoprotein genes drives the emergence of these less fit viruses. Of interest, many of the final gene constellations did not maintain the polymerase complex subunits from the same parent, despite this expectation due to their co-evolution. This study shows that reassortment is largely random process initially, but the selective pressure of gene co-segregation during packaging in addition to viral fitness restricts the final viruses that dominate. Our approach has provided insight into the drivers that dictate gene selection and therefore impact upon progeny phenotype.