ObjectiveTo date, enamel matrix derivative (EMD) has been considered to be one of the few biomaterials for clinical use capable of demonstrating true periodontal regeneration. The aim of this two-center prospective clinical study was to evaluate 2-year outcome of periodontal regenerative therapy using EMD in the treatment of intrabony defects, performed as an ‘advanced medical treatment’ under the national healthcare system in Japan.ResultsPatients with chronic periodontitis who have completed initial periodontal therapy at either of the two dental school clinics were enrolled. Each contributed at least one intrabony defect of ≥3 mm in depth. During surgery, EMD was applied to the defect following debridement. Twenty-two participants (mean age 55.2 years old, 9 men and 13 women) completed 2-year reevaluation, and a total of 42 defects were subjected to data analysis. Mean gains in clinical attachment level (CAL) at 1 and 2 years were 2.9 mm (38% of baseline CAL) and 3.1 mm (41%), respectively, both showing a significant improvement from baseline. There was also a significant reduction in probing depth (PD): mean reductions at 1 and 2 years were 3.2 and 3.3 mm, respectively. There was a progressive improvement in the mean percentages of bone fill from 26% at 1 year to 36% at 2 years. No significant difference in CAL gain at 2 years was found between 3-wall bone defects and other defect types combined. In multiple regression analysis, the baseline PD was significantly associated with CAL gain at 2 years. In this population of patients, the treatment of intrabony defects with EMD yielded clinically favorable outcomes, as assessed by periodontal and radiographical parameters, over a period of 2 years.Electronic supplementary materialThe online version of this article (doi:10.1186/s13104-017-2572-2) contains supplementary material, which is available to authorized users.