Staphylococcus aureus is a bacterial pathogen causing bovine intramammary infections (IMIs) often leading to chronic clinical or subclinical mastitis. Predicting the outcome of S. aureus IMIs (duration and clinical vs subclinical) based on the characterization of isolates would help to make better case management decisions. For this purpose, 583 S. aureus isolates from series of quarter milk samples were characterized by genotypic tests (detection of virulence genes seg, tst, lukM), epidemiological typing (spa type) and by a phenotypic test (biofilm production). VNTR typing (variable number of tandem repeats) was used to establish persistence of the same S. aureus strain in each series of sequential isolates. This allowed to associate each strain to a clinical/subclinical status and to validate the duration of infection. We found differences in the distribution of spa types between the strains from clinical and subclinical cases. Prevalence of lukM was also higher in strains from clinical cases than in strains from subclinical cases. A Kaplan-Meier analysis was then used to determine factors influencing the duration of the infection. Considering a multivariable model of the logistic regression, time to elimination was shorter with the strains of the subclinical lactation series compared to the clinical series (series with at least one clinical case). Strains from the spa type t359 and t529 were less likely to persist compared to those of spa type t13410. In sum, strain characterization including determination of the spa type helps to predict duration of infection and the clinical or subclinical outcome of S. aureus IMIs.