Purpose: Scutellaria baicalensis is a herb which has effect of eliminating heat, drying dampness, purging away fire, detoxicating. Clinically, has been used to remove fever and control of inflammation. We have studied in series to investigate the effective traditional oriental medicines of treatment for endometriosis. In this study, the effects of Scutellaria baicalensis administrated orally or rectally on surgically induced endometriosis in rat were investigated. Methods: The endometrial tissues of rats were autografted to their small intestine. Rats with surgically induced endometriosis were administered with Scutellaria baicalensis extracts for 40 days orally or rectally. We observed the tissue size of ectopic uterine implants at the mesenteric with the naked eye and examined the concentration of estradiol, progesterone, $TNF-{alpha}$ and IL-2, IL-4, IL-6 and IL-10 in serum. Also, we inquired which was more effective between oral administration groups and rectal administration groups. Results: The size of ectopic uterine implants of orally or rectally treated groups was much smaller than those of control groups. The concentrations of estradiol, progesterone, $TNF-{alpha}$, IL-2 and IL-6 were significantly decreased in oral administration experimental group compared with the control group. The concentrations of progesteron, $TNF-{alpha}$, IL-2 and IL-6 were significantly decreased in rectal administration experimental group compared with the control group. The efficiency of oral administration group was better than that of rectal administration group at the serum concentration of estradiol and IL-4. Conclusion: Our data suggest that Scutellaria baicalensis inhibit the inflammation induced from ectopic uterine implants at the mesenteric wall and inhibit the growth of ectopic uterine implants. Judging from the above results, it can be suggested that Scutellaria. baicalensis should be a useful agent for inhibiting the inflammation induced from ectopic uterine implants and the proliferation of endometriosis. Maybe, oral administration of Scutellaria baicalensis is more effective than rectal administration.