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To investigate the possible risk factors and clinical effects of black areas in small-incision lenticule extraction.Thirty-one cases and 126 controls were enrolled in a case–control study from the database of a single center from September 2012 to July 2017. A retrospective analysis of surgical procedures with video and medical records was performed. Logistic regression analysis was used to assess the possible risk factors for black areas between cases with black areas and controls without black areas.In the study, 19 eyes (61.3%) with black areas were associated with the presence of surface debris, 10 of which had repeated suction during docking and centration (P < 0.001). There was a significant difference in the energy of the femtosecond laser used for the cases (133 ± 4.04 nJ) and controls (138 ± 3.26 nJ) (P < 0.001). The odds ratio for the energy of the laser was 0.180 (95% confidence interval, 0.099–0.328, P < 0.001). Eyes with black areas had poorer uncorrected vision at 1 and 7 days and 1 month postoperatively (0.06, 0.01, and 0.00 logMAR, respectively) compared with controls (−0.01, −0.07, and −0.05 logMAR, respectively) (P < 0.005). At month 3, the safety index was lower in the cases (1.14 ± 0.47) compared with controls (1.36 ± 0.28) (P = 0.003). The postoperative spherical equivalent in the cases was more myopic than in controls (P = 0.036), except for month 3 (P = 0.183).Black areas in small-incision lenticule extraction could be caused by repeated suction, presence of surface debris, and a lower energy of the femtosecond laser. These factors could result in rough dissection and slower recovery of visual acuity.