Background: Post-operative pain and swelling are frequently observed after sinus lift procedures. The aim of the present study was a clinical evaluation of swelling and pain of two sinus lift different flaps technique measured through visual analogue scale (VAS), verbal rating scale (VRS) and infrared thermal imaging (i.e., thermography). Methods: A randomized controlled trial was conducted in fifteen patients treated for a total of 30 sinus randomly allotted into two groups. In patients of Group I, a triangular flap was performed, while in Group II modified triangular flap without anterior release was performed. Postoperative pain was scored by VAS and inflammation was recorded by VRS at 2, 4, 6 and 14 days. The facial temperature was recorded before and after sinus augmentation, at 2, 4, 6 day intervals for the first week and at 14 day, to check the course of healing. Results: In group I the pain intensity was recorded at 2 days after the surgery with a score of 38.67 ± 6.4 mm. Swelling was higher at 2 and 4 day, and it was absent at day 6. Facial temperature difference before and after the procedure was 3 (4.737 °C ± 0.37). In Group II the pain was lower than in Group I (p < 0,05). Swelling scored 2 on the first and second day, and it was reduced at day 4. After the second day the difference of temperature reduced significantly compared to day of surgery (0.77 °C), at 2 and 4 days no difference was registered. Conclusion: In conclusion based on the outcome of the present study, modified triangular flap can be used with success in sinus augmentation procedures and is to be preferred to trapezoidal flap.