Objectives Asthma patterns in childhood are important predictors of unwanted outcomes in adolescence. We aimed to define asthma phenotypes in childhood and adolescence and evaluate the transitions between these phenotypes and factors potentially associated with the transitions. Methods Baseline (1445 children), first round (1363 children/early adolescents) and second round (1206 adolescents) data from the SCAALA Project in Salvador, Brazil, were used. Phenotypes were defined by latent class analysis at three time points. Transitions between phenotypes were described and the effects of factors associated with transition probabilities estimated using latent transition analysis. Results The ‘‘asymptomatic’’ and ‘‘symptomatic’’ phenotypes were identified. Approximately 5–6% of asymptomatic children in childhood/later childhood and early adolescence became symptomatic later in time. Maternal common mental disorders were identified as important risk factor for unhealthy states. Conclusions Asthma manifestations are characterized by frequent movements, especially between childhood and adolescence. Our study, by simultaneously defining disease subtypes, and examining the transitions and their potential predictors, highlights the importance of longitudinal studies to advance the understanding of the effects of social, environmental and biological mechanisms underlying asthma trajectories over time.