To assess expression of three main inflammatory genes, COX-II, ALOX-12 and i-NOS, quantitatively at transcriptional level in cholesteatoma matrix tissue. Ten patients who have chronic otitis media with primary acquired cholesteatoma were included in this study. Tissue samples obtained from cholesteatoma matrix and external ear canal skin (control tissue). Expression of the targeted genes (COX-II, i-NOS and LOX-12) was assessed using real-time quantitative polymerase chain reaction (RT-PCR) technique. The amount of COX2 mRNA was significantly higher in cholesteatoma matrix at transcriptional level (p = 0.038). There was no statistically significant difference regarding expression of iNOS and LOX12 mRNA levels (p > 0.05). There is a significant overexpression of the mRNA of COX-II in cholesteatoma matrix, which indicates a difference between the normal skin and cholesteatoma matrix at molecular level. COX-II gene overexpression seems to be associated with pathogenesis of cholesteatoma. This molecular change is similar to the molecular abnormalities observed in some benign and malignant neoplasms. Invasive and locally destructive nature of cholesteatoma may be due to COX-II overexpression. Absence of an increase in the gene expressions of i-NOS and LOX-12 in cholesteatoma matrix suggests that these mediators may not be related with the pathogenesis and evolution of cholesteatoma.