Background: Lower respiratory tract infection (LRTI) often leads to hospitalization, and it was indicated that causative viral infections are underestimated. Objectives: It was our aim to compare the frequency of 8 relevant viruses in 109 hospitalized LRTI patients and 144 healthy controls. Methods: Virus infection was determined by seroconversion and ELISA for anti-virus antibodies in repeated serum samples. Bacterial infection was diagnosed in respiratory specimens, blood cultures and urine. Results: The LRTI patient cohort consisted of 49 patients with community-acquired pneumonia, 30 patients with acute bronchitis and 30 chronic obstructive pulmonary disease patients with acute exacerbation. Viral infection was detected in 89 (82%) LRTI patients compared with 32 (22%) in healthy controls (relative risk 3.42, 95% confidence interval 2.48–4.72; p < 0.0001). The most frequent viral pathogens were: influenza B (23%), adenovirus (16%) and parainfluenza virus 3 (12%). Importantly, infections with more than 1 virus were detected in 63% (n = 57) of LRTI patients with viral infection, which represents 52% of all LRTI patients. No multiple virus infection was detected in the healthy controls. Patients with community-acquired pneumonia were more often infected with adenovirus and respiratory syncytial virus as compared with the other LRTI patients (p = 0.046 and 0.0009, respectively). Conclusions: There is a high incidence of single and multiple viral infections in LRTI patients requiring hospitalization. The data indicate the need for regular virus diagnosis and the development of point of care tools that enables a fast diagnosis of the most common viruses and bacteria. The data also imply the need to consider antiviral therapy in positive LRTI cases.