Regenerative periodontal therapy with an enamel matrix protein derivative (EMD) has been shown to promote regeneration in intrabony periodontal defects. However, in most clinical studies, root surface conditioning with EDTA was performed in conjunction with the application of EMD, and, therefore, it cannot be excluded that the results may also be attributable to the effect of the root conditioning procedure. The purpose of this study was to determine the effect of root conditioning on the healing of intrabony defects treated with EMD. Twenty-four patients, each of whom exhibited one deep intrabony defect, were randomly treated with either open flap debridement (OFD) followed by root surface conditioning with EDTA and application of EMD (OFD+EDTA+EMD) or with OFD and application of EMD only (OFD+EMD). The following parameters were recorded at baseline and at 1 year: plaque index (PI), gingival index (GI), bleeding on probing (BOP), probing depth (PD), and clinical attachment level (CAL). No differences in any of the investigated parameters were observed at baseline between the two groups. Healing was uneventful in all patients. At 1 year after therapy, the OFD+EDTA+EMD group showed a reduction in mean PD from 9.3+/-1.3 mm to 4.0+/-0.9 mm (P<0.001), and mean CAL changed from 10.8+/-2.2 mm to 7.1+/-2.8 mm (P<0.001). In the OFD+EMD group, mean PD was reduced from 9.3+/-1.2 mm to 4.2+/-0.9 mm (P<0.001), and a change in mean CAL from 11.0+/-1.7 mm to 7.3+/-1.6 mm (P<0.001). There were no significant differences in any of the investigated parameters between the two groups. In intrabony defects, regenerative surgery including OFD+EDTA+EMD failed to show statistically significant differences in terms of PD reduction and CAL gain compared to treatment with OFD+EMD.