The objective of the study is to investigate gender differences in the respiratory effects of air pollution in schoolchildren. We studied 1397 schoolchildren from two locations in Egypt; Cairo city with high level of air pollution and Shbeen Al Koom in the Delta with low level of air pollution. Lung function testing was done by the Vitalograph spirometer. The Arabic version of ISAAC questionnaire was used (the International Study of Asthma and Allergies in Childhood). Air pollution measurements were collected from the Government sites in both locations. Boys in Shbeen Al Koom had significantly (p< 0.05) higher lung function tests than boys in Cairo. There was no significant differences in lung function tests between girls in both locations. Children in Cairo had significantly (p< 0.01) higher prevalence rates of asthma, rhinitis and eczema than children in Shbeen Al Koom. The prevalence rates of ever rhinitis were 6% and 3% higher in boys and girls in Cairo compared with Shbeen Al Koom, respectively. Children who developed rash less than 2 years of age were 2% and 5% higher in boys and girls in Cairo compared with Shbeen Al Koom, respectively. The prevalence of other allergic symptoms were 2-3% and 3-5% higher in boys and girls in Cairo compared with Shbeen Al Koom, respectively. The present study shows the adverse respiratory effects of exposure to traffic air pollution on schoolchildren showing gender difference. The study will help to implement strategic health intervention programmes to improve the respiratory health of children.