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The effects of <i>trans</i>-cinnamaldehyde (TC) on transcriptional profiles of biofilm-associated genes and the metabolic activity of two methicillin-resistant <i>Staphylococcus aureus</i> (MRSA) strains showing a different degree of adherence to polystyrene, were evaluated. Metabolic activity of <i>S. aureus</i> in biofilm was significantly decreased in the presence of TC at 1/2 minimum biofilm inhibition concentration (MBIC). Expression levels of the genes encoding laminin binding protein (<i>eno</i>), elastin binding protein (<i>ebps</i>) and fibrinogen binding protein (<i>fib</i>) in the presence of TC at 1/2 MBIC were lower than in untreated biofilm in both the weakly and strongly adhering strain. The highest decrease of expression level was observed in case of <i>fib</i> in the strongly adhering strain, in which the amount of <i>fib</i> transcript was 10-fold lower compared to biofilm without TC. In the presence of TC at 1/2 MBIC after 3, 6, 8 and 12 h, the expression level of <i>icaA</i> and <i>icaD</i>, that are involved in the biosynthesis of polysaccharide intercellular adhesin, was above half lower in the weakly adhering strain compared to biofilm without TC. In the strongly adhering strain the highest decrease in expression of these genes was observed after 3 and 6 h. This study showed that TC is a promising anti-biofilm agent for use in MRSA biofilm-related infections.