Background: Respiratory Syncytial Virus (RSV) is the leading cause of bronchiolitis. The local bacterial ecosystem may influence RSV disease severity and the immune response. Aim: To evaluate the association between RSV infection, nasal microbiota composition (NMC) and patients’ immune response in infants with bronchiolitis. Materials and Methods: We characterized the NMC of 47 hospitalized infants Results: NMC differed among RSV and non RSV groups. In RSV-positive nasal samples alfa-diversity was reduced and NMC differed between RSV-A and RSV-B. Discriminant bacterial species were Clostridium indolis for RSV-A group and Hemophilus haemolyticus for RSV-B. In infants with RSV, there was a significant cross-correlation among NMC (evaluated as β diversity) and white blood cells level, expression of Lambda3 and Beta IFN genes and Th1/Th2 response. Conclusions: This preliminary study showed differences in the NMC in relation to the aetiological cause of bronchiolitis and the type of immune response, that are worthy of further examination in larger groups.