Invasive disease caused by Streptococcus pneumoniae and Staphylococcus aureus is associated with nasal carriage of these bacteria. Use of a pneumococcal conjugate vaccine (PCV) in children altered nasal carriage rates and reduced infections due to S. pneumonia. Similar studies demonstrate that there is an inverse correlation between S. pneumoniae and S. aureus nasal carriage in children, but this inverse correlation has not been extensively investigated adults. The PCV is now approved for use in adults, a group more likely to be colonized with S. aureus. To investigate the impact of PCV vaccination on S. aureus carriage in adults, the clinical evaluation of a multiplex Real Time PCR method to simultaneously detect very low levels of S. pneumoniae and S. aureus from the same nasal sample is described.