BACKGROUND Staphylococcus aureus produces various toxins and enzymes, and its presence can exacerbate skin conditions. Previous studies have shown that S. aureus is involved in skin deterioration, even in normal tissue. Biofilm strains show much greater resistance to antimicrobial agents and therefore require a much higher concentration of biocide than planktonic counterparts. OBJECTIVE As such, alternative strategies and more effective therapeutic agents against biofilm-producing S. aureus in skin are of great interest. Therefore, we turned our attention to differences in 50 clinical biofilm strains isolated from human facial skin. METHODS Based on S. aureus density on facial skin, we divided donors into two groups: relatively low density (LSG) and high density (HSG). In general, strong biofilm-forming strains were detected in the HSG donors. Two strains from each of the groups were submitted to gene microarray analysis to investigate expression differences and confirmed by RT-PCR. RESULTS In total, 111 of 7775 genes were differentially expressed between low (SA2 and SA7) vs. high (SA10 and SA33) biofilm-forming clinical strains. These genes include already well-known as biofilm formation related genes like icaABCD and lrgAB, and newly identified genes (sdrC, sspBCP) by RT-PCR. Comparison of gene expression differences between the two groups available at NCBI Gene Expression Omnibus accession number GSE44268. CONCLUSIONS Our results suggest that S. aureus density in the skin is closely related to biofilm-forming ability, and we have identified several potential target genes that may be involved in regulating biofilm formation in situ.