Background: Hidradenitis suppurativa (HS) is a chronic, recurrent, auto-inflammatory disease that affects the pilosebaceous unit in apocrine gland-bearing areas. Bacteria are thought to play a role in the development and progression of disease. In addition, antibiotics are frequently used as first-line management for HS. We sought to determine the carriage status of Staphylococcus aureus and its resistance to antibiotics among patients with HS in a tertiary referral hospital in Athens, Greece. Methods: In this observational cohort study, 68 consecutive patients attending the HS clinic of “Attikon” General University Hospital in Athens, Greece, during a 9-month period were enrolled. All patients had not received any antibiotic therapy for any reason during the previous 3 months before enrollment. Nasal and oropharyngeal samplingwere obtained, and specimens were tested for the presence of S. aureus.Antibiotic susceptibility testing was performed using the VITEK 2 system. Standard statistical tests, descriptive statistics tests, and χ2 and Pearson correlation tests were performed, using IBM SPSS Statistics 25.The level of significance was set at a pvalue <0.05. Results: Sixty-eight patients with HS were studied. There were 44 females (64.7%) and 24 males (35.3%). The mean age was 36.63 ± 13.0 (IQR = 21), and the mean age at onset of disease was 23.90 ± 11.53 (IQR = 14). The mean duration of disease was 12.74 ± 10.20 years (IQR = 15). Fifteen (22.1%) of the patients were Hurley stage I, 22 (32.4%) were Hurley stage II, and 31 (45.6%) were Hurley stage III. S. aureus carriage was detected in 17 patients (25%). Six of them (35.3%) had MRSA strains. There was an increased prevalence of S. aureus colonization (p = 0.058) and MRSA (p = 0.101) in Hurley stage III patients, but this result was not statistically significant. Conclusions: We found a 25% prevalence of S. aureus colonization (17/68 patients) and a 35.3% prevalence of MRSA (6/17) among our HS patients. There was an increased prevalence of S. aureusand MRSA positivity in HS patients with Hurley stage III. Further studies are needed to clarify the possible clinical significance of S. aureus carriage in the disease development and progression as well as in the treatment outcome.