We have examined the expression profile of the influenza virus PA protein in pH1N1/2009 virus-infected cells. Immunoblotting analysis of virus-infected MDCK cells revealed the presence of full-length PA protein from 8 hrs post-infection, together with the simultaneous appearance of PA protein species of approximately 50 kDa, 35/39 kDa and 20/25 kDa (collectively referred to as PA*). PA* was also detected in H1N1/WSN virus-infected cells indicating that its presence was not virus-specific, and PA* was also observed in virus-infected A549 and CEF cells indicating that its presence was not cell type-specific. PA* was detected in cells expressing the recombinant PA protein, indicating that the PA* formation occurred in the absence of virus infection. These data collectivity indicated that PA* formation is an intrinsic property of PA gene expression. The association of PA* with purified influenza virus particles was demonstrated by immunoblotting, and a protease protection assay provided evidence that PA* was packaged into virus particles. The ribonucleoprotein (RNP) complex was isolated from purified influenza virus particles using glycerol gradient centrifugation, which demonstrated that PA* was associated with the RNP complex. To the best of our knowledge this is the first report to demonstrate that PA protein species containing only segments of the C-terminal domain form during influenza virus infection. Furthermore, these truncated PA protein species are subsequently packaged into virus particles as part of the functional RNP complex.