The present study is aimed to describe the changes in the prevalence of symptoms of asthma, rhinitis and eczema among Brazilian adolescents (AD, 13-14 years old) between Phases 1 and 3 of the International Study of Asthma and Allergies in Childhood (ISAAC). The prevalence of self-reported symptoms of asthma, rhinitis and eczema in AD from five Brazilian cities (Curitiba, Porto Alegre, Recife, Salvador and São Paulo), obtained during ISAAC Phase 1 (n = 15 419) and Phase 3 (n = 15 684), was compared to determine the trend of prevalence in a 7-year interval. There was a trend to reduction in the current prevalence of wheezing and increasing of nocturnal cough when averaging figures from the five cities. The prevalence of wheezing in the last 12 months was 27.7 vs. 19.9% (p < 0.01); asthma ever 14.9 vs. 14.7% (p > 0.05); severe episode of wheezing 5.2 vs. 5.2%; nocturnal cough 32.6 vs. 34.9% (p < 0.01); exercise wheezing 23.6 vs. 23.0% (p > 0.05) and awake with wheezing 11.8 vs. 11.2% (p > 0.05). Similar things were observed with the prevalence of current symptoms of rhinitis and eczema. In Brazil, there was a small but significant mean decrease in the prevalence of two asthma-related symptoms, wheezing and nocturnal cough, though this trend was not consistent in the surveyed cities. The prevalence of asthma symptoms in Brazil, despite its mean trend to a decrease, is still one of the highest in Latin America.