Staphylococcus aureus strains generally colonize eczematous lesions of subjects with atopic dermatitis much more frequently than in the skin of normal individuals. The aim of this study was to provide a detailed genotypic and phenotypic analysis of S. aureus strains colonizing four different sites (lesional and non-lesional skin areas, nasal and pharyngeal mucosas) of 49 patients with atopic dermatitis. The 88 isolates were analyzed in duplicate by pulsed field gel electrophoresis and in their exfoliative toxin A or B production by latex test. The patients were characterized by age, sex, severity scoring of atopic dermatitis and serum eosinophil cationic protein. Fourteen (28.6%) of the patients were completely negative for S. aureus while 35 (71.4%) were positive in at least one site. The severity scores and eosinophil cationic protein levels were significantly correlated variables (P<0.001), linked to the colonization intensity (P ranging between 0.05 and <0.001 depending on the site) and to the number of colonized sites (P at least <0.01). The genotypic patterns, widely heterogeneous, showed no restriction to peculiar patterns. Only eight strains produced exfoliative toxin B which was significantly restricted to the lesional isolates (P=0.012).