Objective The aim of this study was to compare the clinical and radiographic efficacy of guided tissue regeneration with a modified perforated collagen membrane (MPM) or standard collagen membrane (CM) in the treatment of intrabony defects in patients with aggressive periodontitis (AgP). Materials and methods Fifteen AgP patients were included in the study. Two single intrabony defects of at least 3 mm depth with ≥ 6 mm probing pocket depth (PPD) from each patient were randomly assigned to either xenogenic graft plus MPM (test group) or xenogenic graft plus CM (control group). PPD, clinical attachment level (CAL), and gingival recession (GR) were recorded at baseline and at 12 months. The radiographic assessments included the measurements of defect depth (DD), change in alveolar crest position (ACP), linear defect fill (LDF), and percentage defect fill (%DF). Results After treatment, PPD, CAL, DD, and ACP values improved significantly in both groups, without statistical differences between them. However, with respect to LDF and %DF, the 12-month radiographic analysis at MPM-treated sites showed a significant improvement compared to the 6-month outcomes, that was not observed at control sites (additional LDF of 0.4 ± 0.5 mm, p = 0.010 and %DF of 6.4 ± 7.6%, p = 0.025). Conclusions Both strategies proved effective in the treatment of intrabony defects in patients with AgP. Nonetheless, enhanced LDF and %DF 12 months postoperatively at MPM-treated sites may stem from cellular and molecular migration from the periosteum and overlying gingival connective tissue through barrier's pores. Clinical relevance Modification of CM may have positive ramifications on periodontal regeneration.