Rationale The relative contribution of various genetic factors in the development of allergies and asthma is unclear. We investigated the effect of parental history of allergy as collected by survey on the risk of clinical presentation specific allergic phenotypes in children. Methods Allergic phenotypes were categorized in 484 participants in CAS, a prospective birth cohort who completed a physical exam at ages 6-7 years. We compared risk in two phenotype categories which were considered mutually exclusive: atopy without asthma or bronchial hyperreactivity (BHR); asthma with BHR, but no atopy. Odds ratios (OR) and 95% confidence intervals (CI) were calculated and adjusted for confounding factors of birth order, gender and pet exposure. Results Adjusted values indicated that in atopic, non-asthmatic children the risk conferred by having a mother with allergy OR=1.93 (95% CI 1.09,3.40), or a father with allergy 1.88 (95% CI 1.01,3.50) was almost two fold; and the risk increased when both parents had allergies OR=2.27 (95% CI 0.93,5,55). When stratified by gender, the effect of parental history in the atopic phenotype was observed only in girls, and was greater than in the combined group. In the asthmatic phenotype, paternal allergy conferred increased risk, which could be calculated only in boys. Conclusions Parental history has differential effects on the risk of developing allergic and asthmatic phenotypes and these effects may be gender specific.