To gain insights into the evolution of influenza A viruses (IAVs) during infection of vaccinated pigs, we experimentally infected a 3 week-old naive pig with a triple reassortant H1N1 IAV and placed him into direct contact with a group of age-matched vaccinated pigs (n=10). We indexed the genetic diversity and evolution of the virus at an intra-host level by deep sequencing the entire genome directly from nasal swabs collected at two separate samplings during infection. We obtained 13 IAV metagenomes from 13 samples, which included the virus inoculum and 2 samples from each of the six pigs that tested positive for IAV during the study. The infection produced a population of heterogeneous alleles (sequence variants) that was dynamic over time. Overall, 794 polymorphisms were identified among all samples, which yielded 327 alleles, 214 of which were unique sequences. A total of 43 distinct hemagglutinin (HA) proteins were translated, two of which were observed in multiple pigs, whereas the neuraminidase (NA) was conserved and only one dominant NA was found throughout the study. The genetic diversity of IAVs changed dynamically within and between pigs. However most of the substitutions observed in the internal gene segments were synonymous. Our results demonstrate remarkable IAV diversity, and the complex, rapid and dynamic evolution of IAV during infection of vaccinated pigs that can only be appreciated with repeated sampling of individual animals and deep sequence analysis.