Treatment of intrabony periodontal defects with a combination of an enamel matrix derivative (EMD) and a natural bone mineral (NBM) has been demonstrated to significantly improve clinical parameters such as probing depth (PD) and clinical attachment level (CAL). However, long-term clinical and histologic data on treatment with this approach are limited. The aim of the present study was to present the 5-year clinical and histologic results following treatment of intrabony defects with a combination of EMD + NBM. Eleven healthy patients, all with advanced chronic periodontitis and one deep intrabony defect each, were consecutively treated with a combination of EMD + NBM. PD, recession of the gingival margin (GR), and CAL were measured just before and at 1 and 5 years after treatment. The primary outcome variable was CAL. No adverse healing responses were observed. Mean PD, GR, and CAL were significantly reduced at 1 year and at 5 years versus baseline values. Histologic analysis of a mandibular second molar, extracted 5 years after treatment with EMD + NBM, demonstrated bone formation around the NBM particles. Regenerative surgery with the combination of EMD + NBM may result in bone formation, and the obtained clinical results can be maintained over a period of 5 years.