Along with an expanding global swine production, the commercial housing and management of swine herds, provide an optimal environment for constant circulation of swine influenza virus (swIAV), thereby challenging farmers and veterinarian in determining optimal control measures. The aim of this study was to investigate the role of gilts in the swIAV transmission dynamics, and to evaluate the impact of different control measures such as quarantine and gilt vaccination. The study was conducted as a cross-sectional study in ten Danish sow herds, including five swIAV vaccinated and five unvaccinated herds. Blood- and nasal swab samples of gilts, first parity sows, and piglets were collected in different stable units of the production system and analyzed for the presence of swIAV and swIAV antibodies. Associations between the detection of swIAV, seroprevalence, antibody levels, quarantine measures and vaccination strategy were thereafter investigated to identify possible risk factors for swIAV introductions and persistence within the herds.Nine of the ten herds had gilts or litters of first parity sows testing positive for swIAV, and swIAV was detected in both the quarantine, mating- and farrowing unit. The seroprevalence were generally higher in the vaccinated herds, but swIAV was still present in nasal swabs from both gilts and piglets in these herds. Notably, the results revealed that having positive gilts in the end of the quarantine increased the risk of having positive one-week-old litters in the farrowing unit by 2.5 times. These results underline that gilts are important contributors to the continuous circulation of swIAV. Additionally, the recorded vaccination schedules along with quarantine and biosecurity measures were far from optimal emphasizing a needed focus on these factors if control of pathogens such as swIAV is desired.