Background: Hospital-acquired influenza A brings hospitalized patients an additional cost of care and considerable mortality, but risk factors for hospital-acquired influenza A are unknown. We aimed to describe the characteristics of patients vulnerable for hospital-acquired influenza A and to identify its risk factors. This knowledge would help clinicians to control hospital-acquired infection and reduce the burden of treatment.Methods: A case-control study was conducted in hospitalized patients aged ≥18 years in a tertiary level teaching hospital during the 2018–2019 influenza A season. Patient data were retrieved from hospital-based electronic medical records. Hospital-acquired influenza A was defined as a case of influenza A diagnosed 7 days or more after admission, in a patient who had no evidence of viral respiratory infection on admission. The controls without influenza were selected among patients exposed to the same setting during the same time period. We identified risk factors using conditional logistic regression and described characteristics of patients with hospital-acquired influenza A by comparing the clinical data of the influenza patients and the controls.Results: Of 412 hospitalized patients with influenza A from all departments of the study hospital, 93 (22.6%) cases were classified as hospital-acquired. The most common comorbidities of the 93 cases were hypertension (41.9%), coronary heart disease (21.5%) and cerebrovascular disease (20.4%). Before the onset of hospital-acquired influenza A, patients presented more lymphocytopenia (51.6% vs 35.5%, P=0.027), hypoalbuminemia (78.5% vs 57.0%, P=0.002) and pleural effusion (26.9% vs 9.7%, P=0.002) than matched controls. Notably, infected patients had a longer hospital stay (18 days vs 14 days, P=0.002), and higher mortality (10.8% vs 2.2%, P=0.017). Lymphocytopenia (odds ratio [OR]: 3.11; 95% confidence interval [CI]: 1.24–7.80; P =0.016), hypoalbuminemia (OR: 2.24; 95% CI: 1.10–4.57; P =0.027) and pleural effusion (OR: 3.09; 95% CI: 1.26–7.58; P =0.014) were independently associated with hospital-acquired influenza A.Conclusions: Lymphocytopenia, hypoalbuminemia and pleural effusion were independent risk factors that could help identify patients at high risk of hospital-acquired influenza A, which might extend hospital stay and is associated with a high mortality.