Previous systematic reviews have demonstrated better results with enamel matrix derivative proteins (EMDP) as compared with open flap debridement (OFD) for the management of infrabony periodontal defects (IPD). The aim of this study was to determine whether these differences vary according to the follow-up and quality of the studies. Cochrane Central Register of Controlled Trials, Medline/PubMed, Lilacs, Embase and Web of Science electronic databases were searched up to August 2013 for randomized clinical trials.Eligible outcomes were changes in probing depth (PD), clinical attachment level (CAL),gingival recession (GR) and bone changes (BC). Studies with follow-up of 12 months showed differences of 0.97 mm (CI95% 0.52 -1.43) and 1.19 mm (CI95% 0.77 -1.60) for PD and CAL, respectively, favorable for EMDP. Studies with follow-up ≥ 24 months presented advantages of 1.11 mm (CI95% 0.74 -1.48) for CAL and 0.83 mm (CI95% 0.19 -1.48) for PD,with use of EMDP. Considering the quality of studies, those with low risk of bias showed lower difference between groups, presenting 0.8 mm (CI95% 0.24-1.36) for CAL, favorable for EMDP and without differences for PS (0.51 mm, CI95% -0.21 -1.23). In conclusion, follow-up time (< or > 2 years) and the risk of bias influence the results of treatment with EMDP in IPD.