Background Respiratory syncytial virus (RSV), human metapneumovirus (hMPV), and influenza virus infections cause countless adult hospitalizations each year, yet the clinical characteristics and outcomes of RSV and hMPV infections in adults remain poorly understood. This study was thus designed to compare the clinical findings and severity between adult patients hospitalized with RSV/hMPV infections relative to those hospitalized with influenza.Methods This study prospectively enrolled 594 patients that had been hospitalized with influenza-like illness and laboratory confirmed RSV, hMPV, or influenza viral infections over the course of three consecutive influenza seasons at a tertiary hospital in China. In order to identify clinical features associated with these three viral infections and with disease severity, univariate and multivariate logistic regression analyses were conducted. Results Myalgia and lymphocyte counts < 0.8×109/L were positively correlated with the incidence of influenza infection, whereas age ≥ 65 years, nasal congestion, dyspnea, and the presence of solid malignant tumors were positively associated with RSV or hMPV infections. However, none of these variables exhibited good predictive performance as a means of discriminating among patients infected with these three different viruses (AUC < 0.70). After controlling for potential confounding variables, RSV infections in pneumonia patients were associated with a comparable 30-day mortality risk [odds ratio (OR) 1.016, 95% confidence interval (CI) 0.267-3.856, p = 0.982], whereas hMPV infection was associated with a reduced risk of mortality (OR 0.144, 95% CI 0.027-0.780, p = 0.025). In patients without pneumonia, however, 30-day mortality risk in patients infected with influenza virus was comparable to that in patients infected with RSV (OR 1.268, 95% CI 0.172-9.355, p = 0.816) or hMPV (OR 1.128, 95% CI 0.122-10.419, p = 0.916). Conclusions Clinical features of influenza, RSV, and hMPV infections are helpful , but not sufficiently distinct to permit discrimination among these three different infection types, and specific pathogenic testing is thus necessary to understand the etiological basis for disease in patients with influenza-like illness. In addition, disease severity associated with these three types of viral infection was inconsistent when comparing patients with and without pneumonia.