Periodontal surgery can be directed to remove the irritants from the tooth surface and reduce the periodontal pocket. The purpose of this study is to compare the clinical effects after between modified Widman flap and modified flap in periodontal patients. Ninety six molar area teeth of 9 patients were used. One of sextants performed a modified Widman flap, while the other side performed a modified flap. After initial periodontal therapy, the following measurements prior to surgery(baseline) were taken : pocket depth, gingival recession, clinical attachment level, tooth mobility, bleeding on probing. Also these measurements were taken at 4 weeks, 8weeks, and 12 weeks after surgery. Significant decrease of pocket depth was shown in both techniques, and the degree of decrease was significant in modified flap than modified Widman flap at 12 weeks. Significant increase of gingival recession was shown in both techniques, and the degree of increase was significant in modified Widman flap than modified flap at 4 weeks, 8 weeks, and 12 weeks. Significant attachment gain was shown in both techniques, and the degree of increase was significant in modified flap than modified Widman flap at 4 weeks, 8 weeks, and 12 weeks. Significant increase of tooth mobility was shown in both techniques at 4 weeks, but the decrease of tooth mobility was shown at 12 weeks. Greater decrease of bleeding on probing was shown in both techniques at 4 weeks. Modified flap was better than modified Widman flap in the decrease of gingival recession and the attachment gain. These results indicate that modified flap operation is better than modified Widman flap operation in the effect of periodontal treatment.