Background: While the prevalence of asthma in children is decreasing or remaining the same, time-trends in the prevalence of rhinitis in children are not known. Understanding sensitisation trends may help inform about trends in asthma and rhinitis prevalence.Objective: To assess time -trends of wheeze, rhinitis and aero-allergen sensitisation prevalence at 10 years of age we compared two birth cohorts established 12 years apart. To gain insight into differences in disease prevalence we assessed association of family-history, early life exposures and sensitisation with wheeze and rhinitis in each cohort.Methods: The IoW (Isle-of-Wight) and FAIR (Food-Allergy-and-Intolerance-Research) unselected birth cohorts were established in 1989 and 2001 in IoW. Identical ISAAC questionnaire and Skin Prick test data were collected and compared at 10 years of age.Results: Over the 12 year period from 2001 to 2012, prevalence of lifetime-wheeze, current-wheeze, and those ever-treated-for-asthma decreased by 15.9% (45.5-vs-29.6,p<0.001), 3.9% (18.9-vs-15, p=0.020) and 8.2% (31.7-vs-23.5, p=0.001) respectively. Conversely, current-rhinitis and lifetime-rhinitis prevalence increased by 5.5% (22.6-vs-28.1, p=0.004) and 13% (18.6-vs-31.7, p<0.001) respectively. Atopic status remained stable, however house dust mite (HDM) sensitisation decreased by 5.6% (19.2-vs-13.6, p=0.004) and grass sensitisation increased by 3.5% (12.9-vs-16.4, p=0.054). Male-sex, parental history of asthma and HDM sensitisation were significantly associated with lifetime-wheeze in both cohorts while maternal smoking during pregnancy was a significant risk factor only in the earlier IoW-cohort. Parental history of rhinitis and grass sensitisation were significantly associated with lifetime-rhinitis in both cohorts while HDM sensitisation was significant only for the IoW-cohort.Conclusion: Contrasting changes were noted with falling wheeze and HDM sensitisation but rising rhinitis and grass sensitisation prevalence. Changing prevalence of aero-allergen sensitisations may explain the different time trends observed in these cohorts.