Bronchiolitis and preschool recurrent wheeze (PSRW) are common paediatric problems causing significant morbidity and mortality in the first years of life. Respiratory syncytial virus (RSV) and rhinoviruses are the commonest pathogens associated with these illnesses. Why some infants are severely affected, requiring admission to hospital, whilst others experience a simple cold is not fully understood: research has suggested that the innate immune response to these viruses is important. The innate immune system has many components and activation or deficiency in one or many areas may explain the different clinical presentations and disease severities that can occur in these infants. This review will summarize the recent evidence highlighting how RSV and rhinoviruses may modulate the innate immune response in both bronchiolitis and PSRW, and discuss how these illnesses affect the long-term development of the infant lung and the possible susceptibility to persistent airway disease.