Analysis of gene pairs in 40 recombinants derived from influenza A/PR/8/34 and A/HK/8/68 viruses demonstrates that reassortment of gens in recombinant viruses is not completely random with respect to all gene pairs. In particular, recombinants in which P1 and P2 and P2 and P3 genes were derived from the same strain were observed at frequencies much higher than expected. Conversely, recombinants in which P1 and P2 or P2 and P3 were derived from different strains were observed much less frequently than expected. The results suggest that these pairs of genes might be “linked”. Less significant “linkage” was observed within the P1 and NP, P1 and P3, and P3 and NS gene pairs. Examination of all other gene pairs revealed random derivation from the two parental viruses. These observations can be explained either by differential interaction of RNA segments or by a requirement for effective protein-protein interactions for gene products involved in RNA transcription and/or replication.