Previous research on Staphylococcus aureus in pigs focused on livestock-associated methicillin-resistant S. aureus (MRSA) and had qualitative cross-sectional design. This study aimed to elucidate frequency, load and stability of S. aureus nasal carriage in pigs over time and investigated possible associations between carriage and immune response. Nasal swabs were collected three times weekly from 480 tagged adult pigs in 20 Danish production farms. S. aureus and MRSA were quantified on selective media by the most probable number method. Serum levels of IgG against ten S. aureus antigens were quantified in selected pigs by a Luminex assay. All farms were positive for S. aureus and 15 for MRSA, leading to an overall prevalence of persistent, intermittent and non-carriers of 24, 52 and 23%, respectively. Carriage frequency and nasal loads were significantly higher in MRSA-positive farms. Logistic regression modeling revealed the presence of individual pigs characterized by high nasal load (≥10000 CFUs per swab) and stable carriage regardless of farm- and pen-associated factors. On the contrary, humoral response was strongly influenced by these environmental factors. The existence of a minority of shedders contributing to maintenance of S. aureus within farms opens up new perspectives to control MRSA in pig farming.