Viruses are the most common cause of lower respiratory tract infections (LRTIs) in children. Our study aimed to shed light on co-infection by comparing it with the most common single agents, such as respiratory syncytial virus (RSV) and rhinovirus (RV), in terms of epidemiological, clinical, laboratory findings, and cost. This retrospective study analyzed medical records pertaining to infants aged below 5 years, hospitalized with a diagnosis of LRTI with RSV, RV, or co-infection. The study group consisted of 199 children, RSV was detected in 116 patients (58.3%), RV in 46 (23.1%), and co-infections in 37 (18.6%). The average age of patients infected with RV was higher (P = 0.006), and the length of hospital stay of patients infected with RSV was longer (P = 0.03) than that with other agents. There was no significant difference between the groups in terms of oxygen requirement, intensive care unit admission, intubation, and development of complications. The cost was significantly higher in the RSV group (P = 0.02) compared to the other groups. Viral co-infections, RSV, and RV constitute an important part of the etiology in patients aged below 5 years; co-infections do not cause more severe clinical findings compared to single viral agents.