Patients with atopic dermatitis (AD) are often heavily colonized by Staphylococcus aureus, which adversely affects eczema severity. Strategies to control S. aureus in AD include antibiotic and or antiseptics. However long-term efficacy is unclear. In this study we consider extra-cutaneous factors that may cause S. aureus re-colonization in adult AD. Twenty-one patients with AD were recruited and were assessed for: duration of AD, use of topical or oral antibiotic within the preceding 3 months, the number of hospital admissions during the preceding year and current treatment. The types of topical treatments used, vehicle, container and the expiry dates were also recorded. The severity of AD was assessed by SCORAD index. Microbiological assessment for S. aureus carriage from affected skin, anterior nares, emollient and topical steroid was undertaken using culture, Staphaurex test and antibiotic resistance. Of the patients 86% had S. aureus colonization. The median SCORAD score were greater in those colonized with S. aureus (P = 0.02) and those with contaminated treatments (P = 0.05). Prior antibiotic treatment, prior hospital admission and nasal carriage did not influence the median SCORAD. Three extra-cutaneous mechanisms by which S. aureus can re-colonize the skin were identified: antibiotic resistance, nasal carriage and treatment contamination.