Previous studies have suggested an association between maternal smoking during pregnancy and asthma symptoms such as wheezing during childhood. However, few have evaluated this association in adolescence, especially in populations with high prevalence of wheezing as in Brazil. Using the 1993 Pelotas birth cohort, a longitudinal study set in southern Brazil of 5249 urban live births, we aimed to evaluate the association between maternal and the partner's smoking during pregnancy and wheezing at 11 and 15 years of age. We evaluated smoking during pregnancy using number of cigarettes/day, and our main outcomes were as follows: wheezing in the last year and number of wheezing crises, at both 11 and 15 years of age, as well as persistent wheezing (having crises at 11 and 15 years of age) and medical asthma diagnosis at age 15. In addition, other socio-demographic variables were included as possible confounders and mediators of this association. We used Poisson regression models to evaluate crude and adjusted associations. Of the 5249 live births in 1993, 87.5% and 85.7% were followed-up to 11 and 15 years of age, respectively. Maternal smoking during pregnancy showed a dose-response association with number of wheezing crises at age 15 (P=0.023), presence of persistent wheezing (P=0.034) and asthma diagnosis (P=0.023). Partner's smoking was not associated with any wheezing variables. Maternal smoking during pregnancy appears to exert an effect on respiratory morbidity of adolescents, evaluated by wheezing symptoms.