Introduction: This analysis was conducted with the objective of evaluating association between waterpipe passive smoking exposure and asthma, and allergies among Lebanese children. Material and methods: Data were taken from a crosssectional study on children from public and private schools. A sample of 22 schools participated in the study, where standardized written core questionnaires were distributed. From 5 to 12-year-old students filled in the questionnaires at home, while 13–14-year-old students filled it in in the class. In total, 5522 children were evaluated for the prevalence of asthma, allergic rhinitis and atopic eczema, and their associated factors, including waterpipe exposure due to parents’ smoking. Results: The descriptive results of parental smoking were, as follows: among mothers: 1609 (29%) mothers smoked cigarettes, 385 (7%) smoked waterpipe and 98 (1.8%) smoked both; among fathers: 2449 (44.2%) smoked cigarettes, 573 (10.3%) smoked waterpipe and 197 (3.5%) smoked both. Maternal waterpipe smoking was significantly and moderately associated with allergic diseases (p < 0.001; ORa = 1.71), including probable asthma, rhinitis and dermatitis (p < 0.001 for all). Quite on the opposite, father’s waterpipe smoking was not associated with any of the diseases. Parental cigarette smoking demonstrated some positive effects: father’s cigarette smoking did not show association with dermatitis or asthma diagnosed by a physician, while mother’s cigarette smoking showed a positive association only with probable asthma. Moreover, no interactions between cigarette and waterpipe smoking were observed. Conclusions: Maternal waterpipe smoking should be regarded as a high risk behavior; however, additional studies are necessary to confirm this finding.