The Staphylococcus aureus cell surface protein clumping factor A (ClfA) and the enzyme sortase A (SrtA), which attach surface proteins to the cell wall, have both been shown to be virulence factors in models of septic arthritis and sepsis. The mRNA levels of clfA, srtA and the putative housekeeping gene gyrase B (gyrB) in S. aureus were determined using real-time PCR during the course of sepsis/septic arthritis. Expression was measured in joints, being a target of localized infection, and in kidneys, representing a systemic compartment. In infected kidneys, the mRNA levels of clfA, srtA and gyrB were all decreasing over time, from day 3 of infection to day 14. The transcript numbers of clfA and srtA decreased faster in septic mice than in mice with a non-septic disease. The mRNA levels of clfA and gyrB in joints, though, were increasing during the course of infection. These differences suggest that the specific tissue environment is decisive for the differentiation of staphylococci. Also, there was a negative relationship between bacterial load in a tissue and the numbers of clfA, srtA and gyrB transcripts per colony-forming unit. Possibly enters the majority of bacteria a metabolically dormant steady state at high bacterial loads.