Summary Background A strong link between disease severity and Staphylococcus aureus colonization of the skin has been reported in patients with atopic dermatitis (AD). Objectives To examine temporal variations in S. aureus colonization and S. aureus CC type in patients with AD, and to investigate links to disease severity, skin barrier properties and filaggrin gene (FLG) mutations. Methods This was a follow‐up study of a cohort of 101 adult patients with AD recruited from an outpatient clinic. Bacterial swabs were taken at baseline and follow‐up from lesional skin, nonlesional skin and the nose. Swabs positive for S. aureus were characterized by spa and the respective clonal complex (CC) type was assigned. Patients were characterized with respect to disease severity Scoring Atopic Dermatitis (SCORAD), skin barrier properties transepidermal water loss (TEWL), pH and FLG mutations. Results In total, 63 patients participated in a follow‐up visit. Twenty‐seven patients (43%) were colonized at both visits, 27 were colonized at only one visit and nine (14%) were not colonized at either visit. Of patients colonized at both visits, 52% remained colonized with the same CC type at follow‐up. Change in CC type was related to an increase in SCORAD of 10·7 points; patients who carried the same CC type had a reduction in SCORAD of 4·4 points. Significantly higher skin pH was found in patients colonized at both visits, while change in CC type was not related to TEWL, pH or FLG mutations. Conclusions The data indicate that temporal variation in S. aureus CC type is linked to flares of the disease. What's already known about this topic? Patients with atopic dermatitis (AD) have a predisposition to skin infections with Staphylococcus aureus. Skin barrier impairments in AD associate with S. aureus colonization. Staphylococcus aureus is strongly linked to disease severity in AD. What does this study add? Change in S. aureus CC type is related to increased disease severity. Staphylococcus aureus CC types undergo temporal variation in less than half of the colonized patients. Respond to this article