Background/Objectives: With the increase in rates of methicillin-resistant Staphylococcus aureus (MRSA) skin infections in the general population, there may be a similar increase of such infections in patients with atopic dermatitis (AD). There are few studies on MRSA prevalence in the AD population, and no previous studies in Australia. This study investigated the prevalence of MRSA and other organisms in the paediatric AD population over the previous 15 years. Methods: Skin swab results and other significant data, including patients' characteristics and comorbidities, were collected on patients with AD aged 0-18 years, admitted to a large teaching hospital in South Australia from 1999 to 2014 (N = 298). This longitudinal, retrospective study investigated, using logistic regression, the change of prevalence of MRSA, methicillin-sensitive S. aureus (MSSA) and Streptococcus spp. in AD over the past 15 years. Results: Compared with 1999-2002, in 2003-2006 patients were approximately threefold more likely (P = 0.350), in 2007-2010 they were approximately 13-fold more likely (P = 0.030) and in 2011-2014 they were approximately 24-fold more likely to test positive for MRSA (P = 0.008), despite low absolute MRSA numbers. There was a positive association between the number of previous hospital admissions per patient and MRSA (OR = 1.16 [1.08-1.25], P = 0.000). In contrast, there was no change in the prevalence of MSSA or Streptococcus spp. over time. Conclusion: The prevalence of MRSA in children with AD is clearly on the rise. This has negative consequences for individuals with AD and is also a major public health problem.