Purpose: To investigate the effect of lateral sinus floor elevation (LSFE) on sinus membrane (SM) thickness and sinus health in mucosa thickness < 5 mm and > 5 mm. Materials and Methods: LSFE was performed in a prospective controlled clinical trial on two groups with < 5 mm and > 5 mm SM thickness (Groups A and B, respectively) and followed for 6 months. Using preoperative and 6-month postoperative CBCT scans and clinical evaluation, SM thickness changes (primary outcome variable), sinus health, augmented bone height and length (augmentation adequacy), membrane-related variables, and operation time were measured. Results: Forty unilateral sinus augmentations (n = 20 for both groups) were performed on 40 subjects (72.5% men, mean age of 48.8 ± 7.6 years), and 52 implants were simultaneously placed. The mean preoperative and 6-month SM thicknesses were 1.4 ± 0.9 mm and 1.3 ± 0.6 mm in Group A, respectively, and were 6.8 ± 1.0 and 3.4 ± 1.7 mm in Group B, respectively. The mean postoperative SM thickness significantly decreased (P < .001) only in Group B. The mean SM thickness changes also revealed a noticeable difference between the two groups (P < .001). Augmentation adequacy and membrane perforation rate were similar in both groups. Clinical and radiographic rhinosinusitis was not detected in any of the patients. Bleeding during separation and resistance to elevation were significantly higher in Group B than in Group A (P = .003, P = .001). Surgical time was longer in Group B (12.08 ± 8.26 minutes) than in Group A (8.64 ± 3.70 minutes), without reaching significance (P = .097). Conclusions: LSFE in thickened mucosa (< 10 mm) and thinner mucosa (< 5 mm) does not cause abnormal changes in the SM and sinus health. LSFE in thickened mucosa results in adequate sinus augmentation. The thickened membrane does not appear to be a contraindication to LSFE.