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The aim of the study was to assess the influence of flap designs (Envelope flap (EF) and Szmyd flap (SF)) for impacted mandibular third molar extraction, on periodontal pocket depth (PPD), clinical attachment loss (CAL) and bone levels (BL) of second molar. Sixty patients indicated for third molar extractions with healthy second molars were allocated into two groups: EF and SF (n = 30). Third molars were assessed for angulation, root patterns, depth of impactions and relation with ramus (Pell and Gregory classification). Extraction of third molars was performed and PPD, CAL and BL around second molars at 0, 3 and 6 month (mon) follow-ups (FU) were assessed clinically and radiographically. ANOVA, Chi-square and Fisher’s exact test were employed to compare periodontal factors between EF and SF groups, considering p ≤ 0.05 as significant. Sixty participants with a mean age of 23.22 ± 3.17 were included in the study. Based on angulation, the most common impaction in the EF and SF groups was mesio-angular (EF, 50%; SF, 36.7%). Buccal and distal PPD showed a significant increase (p < 0.001) in both EF and SF patients from baseline to 6 mon. EF patients showed significantly higher distal and buccal CAL (6.67 ± 0.18 mm; 6.91 ± 0.17 mm) and BL (7.64 ± 0.16 mm; 7.90 ± 0.15 mm) as compared to SF patients (CAL, 6.76 ± 0.26 mm; 6.91 ± 0.17 mm-BL, 7.42 ± 0.38 mm; 7.34 ± 0.34 mm) at 6 mon FU. SF showed better soft tissue attachment (PPD and CAL) and bone stability (less bone loss) around second molars compared to EF after third molar extractions regardless of the patient, tooth and operator factors.