Background: Hospital-acquired influenza potentially leads to significant morbidity and mortality in already vulnerable patients, but its overall burden is not fully understood. We undertook this study to estimate the incidence and trends of hospital-acquired laboratory-confirmed influenza among adults, and to compare clinical characteristics between hospital-acquired and community-acquired influenza cases. Methods: This was a prospective surveillance study over 11 years of adults with influenza-like-illness (ILI) hospitalized in surgery, medicine and geriatric wards in a tertiary acute-care hospital in Lyon, France. Nasal swabs were systematically collected from those with ILI and tested for influenza by reverse transcriptase-polymerase chain reaction at the national influenza reference laboratory (Lyon, France). Results: Influenza was laboratory confirmed at a rate of 1 in 13 patients who developed ILI during their hospitalization. Having an underlying disease was an important characteristic of hospital-acquired ILI cases. Cardiovascular disease was the most frequent underlying condition in both influenza-positive and influenza-negative patients. Complications were more frequent for influenza-positive than influenza-negative patients. The influenza incidence rate was highest in the geriatric ward and increased over the study period. Conclusions: Hospital-acquired influenza poses a significant risk to already vulnerable patients. Longitudinal surveillance data are essential to support better recognition and monitoring of viral infections in hospitals.