BACKGROUND Subjects with atopic syndrome often perceive symptoms from various organs. A single drug that acts on all the syndrome's manifestations would be the ideal treatment. The role of montelukast, a cysteinyl-leukotriene receptor antagonist, is established in treating allergic rhinitis and asthma, but its ability to alleviate atopic symptoms outside the airways is controversial. Our aim was to assess if montelukast could be used to treat all the various symptoms seen in subjects with atopic syndrome. METHODS A randomised, double-blind, placebo-controlled crossover study on the effect of montelukast in atopic syndrome was conducted during the 2007 pollen season. Forty-five pollen-sensitised subjects who had allergic symptoms from both the upper and lower airways and allergic symptoms outside the airways (conjunctivitis, oral symptoms, eczema and/or urticaria) were recruited. The primary outcome parameter was the allergic symptoms, which were assessed using a questionnaire. Secondary outcome parameters were lower-airway inflammation (exhaled nitric oxide) and the need for rescue medication (inhaled beta2-agonists and oral antihistamines). RESULTS There were no differences between montelukast and placebo treatments in allergic symptoms, in exhaled NO concentration or in the need for oral antihistamines. The need for inhaled beta2-agonists was significantly lower during montelukast treatment. CONCLUSIONS Montelukast was not effective in treating allergic symptoms outside the airways in subjects suffering from different manifestations of the atopic syndrome. Based on the current results, montelukast should not be recommended as a general drug to treat all the symptoms of atopic syndrome, but it should be considered as a drug for asthma and rhinitis.