The spectrum of acute symptoms in young outpatient children with respiratory tract infection (RTI) is variable, and it cannot be explained by the diagnosis of acute otitis media (AOM) versus uncomplicated RTI. We studied that the variation of symptoms is explained by the nasopharyngeal bacteria and/or respiratory viruses. Children aged 6-35 months with acute symptoms with AOM (n = 201) or without AOM (n = 225) were eligible in this cross-sectional study. We analyzed their nasopharyngeal samples for pathogenic bacteria by culture and for respiratory viruses by polymerase chain reaction. We surveyed 17 symptoms (fever, respiratory, ear related, nonspecific, gastrointestinal) with a structured questionnaire. Fever had a positive association with influenza viruses odds ratio (OR): 6.61; 95% confidence interval (CI): 1.66-26.27, human metapneumovirus (OR: 3.84; 95% CI: 1.25-11.77), coronaviruses (OR: 3.45; 95% CI: 1.53-7.75) and parainfluenza viruses (OR: 2.18; 95% CI: 1.07-4.47). Rhinitis (OR: 5.07; 95% CI: 1.93-13.36), nasal congestion (OR: 2.03; 95% CI: 1.25-3.31) and cough (OR: 1.91; 95% CI: 1.15-3.17) had positive associations with Moraxella catarrhalis. Furthermore, cough had a positive association with respiratory syncytial virus (OR: 7.20; 95% CI: 1.59-32.71) and parainfluenza viruses (OR: 2.79; 95% CI: 1.02-7.69). The variation of acute symptoms in young children may be influenced by both nasopharyngeal bacteria and respiratory viruses. Our results showed a strong association between fever and respiratory viruses; rhinitis, nasal congestion and cough were associated with M. catarrhalis in the presence of viruses. Further studies are required to determine the possible synergistic role of M. catarrhalis in symptoms of RTI.