Objective: Airway interactions between viruses, especially rhinoviruses, and potentially pathogenic bacteria (PPB; Streptococcus pneumoniae, Haemophilus influenzae, and Moraxella catarrhalis) in early infancy may increase the risk of subsequent wheezing and asthma. We evaluated the association between rhinovirus and PPB in the first 3 months of life and wheezing episodes before age 2 years and asthma at age 5–7 years. Methods: An Australian community-based birth cohort of healthy children involved parents collecting nasal swabs weekly and completing symptom diaries daily until age 2 years. In a follow-up subset, asthma diagnosis was assessed annually until age 7 years. Swabs were analyzed by real-time polymerase chain reaction assays. Children were included if they returned symptom diaries beyond age 3 months (wheeze) or were reviewed at age 5–7 years (asthma). Results: 1440 swabs were returned by 146 children in the first 3 months of life. Wheeze and asthma outcomes were recorded for 146 and 84 children, respectively. Each additional week of rhinovirus detection increased the incidence of wheezing before age 2 years by 1.16 times (95% confidence interval [CI]: 0.99–1.35). There were no significant associations between bacteria and wheeze. Each additional week with H. influenzae increased the odds of asthma at age 5–7 years by 135% (odds ratio: 2.35, 95% CI: 0.99–5.58). No significant interaction was observed between rhinovirus and PPB for wheezing or asthma. Conclusion: Early life rhinovirus infection was associated with wheezing before age 2 years and H. influenzae with asthma by age 5–7 years. Microbes may play an etiologic role in wheezing and asthma, warranting further study.