PURPOSE: To investigate the influence of lateral window sinus augmentation on sinus physiology, including sinus membrane thickness and the outcome of antral pseudocysts. MATERIALS AND METHODS: This retrospective study was performed by reviewing all lateral window sinus augmentation procedures, which were done between the years 2013 and 2015. Each enrolled patient had CBCT images preoperatively (T0), immediately postoperatively (T1), and 6 months postoperatively (T2). The sinus membrane thickness, pseudocyst dimensions, and intraoperative perforation were evaluated. Patient-related factors such as age and sex that could influence the mucosal properties were also analyzed. RESULTS: Based on established inclusion criteria, 306 patients with 320 sinuses were included in this study. The overall mean thickness of the sinus membrane (T0) was 1.30 ± 1.08 mm, and membrane thickening (> 2 mm) was observed in 22.19% of the sinuses. Preexisting pseudocysts were identified in 24 sinuses (7.50%), most of which remained unchanged or disappeared after 6 months. The intraoperative membrane perforation rate was lowest (1.96%) when the membrane thickness was 1.0 to 1.5 mm, and the perforation rate was increased in patients with thickened (> 2 mm) or thinned (≤ 1 mm) membrane. Membranes swelled immediately after operation (T1 vs T0, P < .01) and gradually recovered at 6 months. No significant change in membrane thickness was shown after the sinus augmentation procedure in the perforation group and pseudocyst group. The mean thickness of the sinus membrane at T0 and T1 was significantly higher for male subjects (P < .01). CONCLUSION: Lateral window sinus augmentation has little or no impact on sinus membrane thickness and antral pseudocysts after a 6-month healing period, except for a transient mild membrane swelling. Thickened and thinned membrane were risk factors for intraoperative perforation. Small-sized perforation and pseudocysts might not contraindicate sinus augmentation from the standpoint of the surgical impact on the sinus membrane.