The aim of this study was to monitor Staphylococcus aureus colonization and disease severity in adults with atopic dermatitis (AD) during 5 months. Twenty-one patients attended 3 visits each for severity SCORing of Atopic Dermatitis (SCORAD) assessment, quantitative cultures from the skin and conventional cultures from the anterior nares, tonsils and perineum. S. aureus isolates were typed for strain identity with pulsed-field gel electrophoresis (PFGE). Seventy-one percent of patients were colonized with S. aureus on lesional skin at least once. Density (colony-forming units (CFU)/cm2) was higher on lesional skin than on non-lesional skin (p < 0.05). Density on lesional skin and number of colonized body sites were positively correlated with SCORAD (p = 0.0003 and p = 0.007, respectively). Persistent carriers of the same strain on lesional skin had higher mean SCORAD index than intermittent/non-carriers (36.3 and 17.1, respectively, p = 0.002). The results show a temporal correlation between several aspects of S. aureus colonization and disease severity in AD raising the question of the importance of this in pathogenesis and treatment.