Recent clinical study shows that periodontal regeneration therapy using enamel matrix proteins (Emdogain; EMD) is expected to have the same therapeutic effect as guided tissue regeneration (GTR). However, reports on the combined effect of both therapies are limited, and the clinical significance is not definite. In this study, clinical effects were studied by comparing a combination of EMD and GTR using a collagen membrane for intrabony defects with GTR monotherapy and EMD monotherapy. Sixty-one patients with 69 intrabony defects were included. Efficacy of treatment was evaluated at 6 months and 1 year by assessment of reduction of probing depth, probing attachment gain, and radiographic bone gain. There were no statistically significant differences between presurgical soft tissue measurements and defect characteristics for the three treatment groups. The results showed no significant differences in reduction of probing depth, probing attachment gain, or radiographic bone gain between the three treatment groups at both evaluation times. The combination of GTR using a resorbable membrane for intrabony defects and EMD did not enhance the therapeutic effect compared with each monotherapy.