To investigate the expression of messenger RNA (mRNA) for membrane type-2 matrix metalloproteinases ( MT2-MMPs) and MT3-MMP and compare their expression pattern in women with severe endometriosis and normal controls. Methods Quantitative competitive polymerase chain reaction was performed to evaluate the mRNA expression of MT2-MMP and MT3-MMP in endometrium from 36 women with severe endometriosis and 52 women without endometriosis throughout the menstrual cycle. Results Eutopic endometrium from women with endometriosis expressed higher levels of MT3-MMP than that from normal women in secretory phase ( P < 0.05). MT2-MMP expression from eutopic endometrium showed no significant differences between patients with endometriosis and controls. Conclusion These results suggest that eutopic endometrium from patients with endometriosis may be more proteolytic, angiogenic and prone to growth because of greater MT3-MMP expression than endometrium from women without endometriosis. Thus, increased proteolytic and angiogenic activities may be one of the explanations of the pathogenesis of endometriosis.