The aim of this study was to evaluate the interaction between the exclusive breast-feeding protective effect and the exposure to tobacco smoke at domicile in the first year of life, on the onset of respiratory allergy (asthma and rhinitis) in children until 5 yr of age. This is prospective cohort study, observational, institutional based. Three hundred children born in a public hospital of Salvador-Bahia (Brazil) were followed from birth to 5 yr of age. Data from 268 children at 60 months of life were analyzed. Occurrence of allergic symptoms were studied and correlated with gender, allergic relatives in first degree, exclusive breast-feeding duration, smoking mother, and presence of other smoker at home, considering the first year of life. Exclusive breast-feeding for at least 6 months showed a protection effect against the onset of respiratory allergy in children from birth to 5 yr (p < 0.05); odds ratio (OR): 0.33 (95% CI: 0.18-0.59). Breast-fed children for less then 6 months compared with those breast-fed for 6 months or more, presented a higher risk (OR: 2.34-95% CI: 1.4-3.74) for developing allergic respiratory symptoms just to 5 yr. The protective effect of exclusive prolonged breast-feeding on the onset of respiratory allergy in children from birth until 5 yr was lost when their mothers were smokers (OR: 2.50-95% CI 1.19-5.19). Therefore, the protective effect of breast-feeding in the first year of life on the onset of allergic symptoms until the age of 5 yr was confirmed. This study proposes a confounding effect of maternal smoking on this protection, exposed by a higher risk for present allergic symptoms until the age of 5 yr, in children exclusively breast-fed for 6 months or more, when their mothers smoked.