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Unlabelled: Staphylococcus aureus skin colonization in atopic dermatitis (AD) patients exacerbates disease activity. Nasal and throat S. aureus carriage may be also implicated in the clinical course of allergic rhinitis and asthma. The aim of the study was to evaluate the frequency of skin, nasal, throat S. aureus colonization in patients with AD and asthma and assess if presence of this bacteria on the skin may be related with degree of sensitization., Material and Methods: Swabs for microbiological analysis were taken from affected skin, anterior nares and throat from 40 children with AD, 59 children with asthma and 56 healthy controls. Following lymphocyte subsets: CD3+, CD4+, CD8+, CD3+CD25+, CD4+CD25+ were measured using flow cytometry., Results: Nasal and throat S. aureus colonization was more frequent in atopic children. S. aureus was found in the skin lesions in 97.5% examined children with AD. Percentage of CD8+ was decreased but the number of CD4+, and CD4+CD25T+ cells was elevated compared with healthy. Total IgE and sIgE Der. pteronyssinus and Der. farinae as well SPT (Skin Prick Test) wheel size were higher in AD children compared to asthma. SCORAD was correlated with total and sIgE (mite, pollen) and number of S. aureus and increasing skin reactivity skin. The degree of sensitization was correlated with patient's age, duration of AD and asthma and number of CD3+, CD4+ and percentage of CD4+CD25+ only in AD patients. Severity of asthma was correlated with FEV1 and total IgE., Conclusions: Staphylococcus aureus skin colonization in AD children increases disease activity and degree of sensitization measured by SPT wheel size and results in imbalance of peripheral blood T cells.