Children with atopic dermatitis are more frequently colonized with Staphylococcus aureus than children without atopic dermatitis. However, little epidemiological data exist regarding the prevalence of methicillin-resistant S. aureus among children with atopic dermatitis. Recent studies have revealed an increasing prevalence of community-associated methicillin-resistant S. aureus among patients presenting to hospitals with serious bacterial infections, particularly those with cutaneous and soft tissue infections. As many atopic dermatitis patients are treated empirically with antibiotics for secondary skin infections, an understanding of the epidemiology of bacterial colonization and superinfection is essential for directing proper treatment in the atopic patient population. This study investigates the prevalence of risk factors for community-associated, methicillin-resistant S. aureus colonization among pediatric atopic dermatitis patients encountered at an academic pediatric dermatology clinic. An observational cross-sectional study was conducted at the Children's Hospital of Philadelphia in which 54 patients previously diagnosed with atopic dermatitis were enrolled. A detailed patient questionnaire, a complete cutaneous examination, and an evaluation of eczema severity according to the Eczema Area and Severity Index were completed at the time of enrollment. Bacterial cultures from the skin and nares were obtained to determine the frequency of colonization with either methicillin-sensitive S. aureus or methicillin-resistant S. aureus. Although most atopic dermatitis patients studied were colonized with S. aureus (43/54 [80%]), methicillin-resistant S. aureus was isolated from only seven atopic dermatitis patients (7/43 [16%]). Patients colonized with S. aureus were more likely to be male, to have been previously hospitalized, to have used a topical calcineurin inhibitor in combination with a topical steroid, and less likely to have used topical antibiotics. Bivariable analysis, however, revealed that only previous hospitalization was independently associated with an increased risk of methicillin-resistant S. aureus colonization. We observed that 80% of atopic dermatitis patients were colonized with S. aureus, and that of these patients, 16% of colonized patients were colonized with a methicillin-resistant strain. Methicillin-resistant S. aureus colonization was found to be significantly associated with previous hospitalization. Evidence also indicates that topical calcineurin inhibitors used in conjunction with topical steroids is associated with increased S. aureus colonization, while topical antibiotic use appears to decrease S. aureus colonization.