There is a lack of evidence for treatment of newly diagnosed asthma, and they are based mainly on expert opinion. This pilot study was aimed at evaluating the effects of inhaled corticosteroid (ICS) in two different doses and montelukast sodium on clinical symptoms and lung function in children with newly diagnosed asthma. This was a randomized, double-blind, parallel-group, 12-month pilot trial, studying the effects of budesonide 800 mcg/day and 400 mcg/day and montelukast 5 or 10 mg tablet according to age on clinical symptoms and lung function in 60 children with newly diagnosed asthma. After 6 months of treatment with different doses of inhaled budesonide and montelukast sodium, asthma control and lung function significantly improved in all three groups of treatment; there were no differences between groups. We found significant correlation between time of enrollment and individual answer to the treatment in montelukast group only; children enrolled later (at the end of heating season) responded better to treatment. The answer to both ICS doses was independent from time of enrollment. The results of the present pilot study suggest that natural exposure, even to perennial allergens, should be considered in choosing the initial asthma treatment. We showed that montelukast may be used as initial asthma therapy in children allergic to house-dust mites preferably at the end of the heating season. Therefore, ICS could be a better choice as initial asthma therapy during maximum allergen exposure.