Highly pathogenic avian influenza viruses (HPAIVs) derive from H5 and H7 low pathogenic avian influenza viruses (LPAIVs). Although insertion of a furin-cleavable multibasic cleavage site (MBCS) in the hemagglutinin gene was identified decades ago as the genetic basis for the LPAIV-to-HPAIV transition, the mechanisms underlying the occurrence of insertion are unknown. Here, we show that transient H5 RNA structures, predicted to trap the influenza virus polymerase on purine-rich sequences, drive nucleotide insertions, providing empirical evidence of RNA structure involvement in MBCS acquisition. Introduction of H5-like sequences and structures into an H6 hemagglutinin resulted in MBCS-yielding insertions. Our results show that nucleotide insertions that underlie H5 HPAIV emergence result from an RNA structure–driven diversity-generating mechanism, which could also occur in other RNA viruses. High-pathogenicity influenza viruses have not only been devastating the planet’s wild and domestic bird populations, but they also represent a persistent threat of initiating a fatal human influenza pandemic. Funk et al. investigated how recombination of low-pathogenicity viruses is prone to incorporating sequences for the furin multibasic cleavage site in the hemagglutination gene, which promotes cell invasion by virus. The authors found that transient RNA structures in the virus replication machinery caused it to stutter on adenine-/uridine-rich sequences and allowed the nucleotide insertions that translate into the cleavage site. The authors suggest that these sorts of transient structures might also be present in other RNA viruses. —Caroline Ash