This two-year study investigated the epidemiology of nasal colonization with methicillin-resistant Staphylococcus aureus (MRSA) among patients and healthcare workers (HCWs) in two wards with a high frequency of MRSA isolation, at Hospital Geral de Santo António (HGSA), Portugal. Three point-prevalence surveys per year were carried out. A case-control approach was used to identify potential risk factors associated with MRSA carriage among patients. Incidence rates and risk factors of MRSA carriage among HCWs who were negative at the baseline observation were estimated. Prevalence of MRSA carriage among 276 patients screened was 5.1%. Admission to HGSA or attendance to the Diabetic Foot Outpatient Unit (DFOU) of HGSA within the past 12 months, and previous MRSA isolation were significant risk factors for MRSA carriage. Among HCWs (n = 126), the prevalence of MRSA carriage was 4.8% and the incidence rate was 61/1000 person-years. Nurses and nurse aids were the HCW categories with the highest risk of becoming colonized with MRSA over time (p = 0.01). One HCW chronically colonized was detected. Molecular typing revealed a clonal identity for isolates recovered from patients and HCWs of the same wards, with 88.6% of isolates belonging to the EMRSA-15 (ST22-MRSA-IV) clone.