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The aim of this study was to compare a transposed with a repositioned flap by assessing the periodontal effects on the second molar and primary healing after extraction of partially impacted lower third molars. A total of 24 patients requiring partially impacted mandibular wisdom tooth removal were enrolled in the study. The test group (n = 12) underwent a transposed flap procedure, whereas the control group (n = 12) underwent a repositioned flap procedure. Plaque index, probing depth, bleeding on probing, and width of keratinized tissue were recorded the day of surgery (T1) and after 60 days (T4). Wound dehiscence was assessed on the mesio-distal and bucco-lingual directions at days 2 (T2), 7 (T3), and T4. No significant differences have been observed in the periodontal parameters between the groups at T1 and T4 (P > 0.05). Similarly, no difference was found at T2, T3, and T4 in wound dehiscence incidence (P > 0.05). To date, no data exists on the use of transposed flaps in third molar surgery; thus a comparison of results cannot be done. Further studies with larger population are needed to investigate the potential advantages of this type of flap.