AIM: To investigate the predictive factors of the opaque bubble layer (OBL) compared to the fellow eye of same patients in FS200 femtosecond laser assisted laser in situ keratomileusis (FS-LASIK). METHODS: This study consisted of 60 consecutive patients (120 eyes) with unilateral OBL during FS-LASIK. Eyes were divided into OBL (the OBL eyes) and OBL-free groups (the fellow eyes) based on the occurrence of OBL. The preoperative demographic data, refraction, keratometry, corneal astigmatism, pachymetry, intraocular pressure and intraoperative data including the outlet location of gas diffusing canal were collected. Conditional logistic regression analysis was performed to find the associated factors with OBL in the two groups by determining odds ratios (OR) and 95%CI. RESULTS: The preoperative demographic data, mean spherical errors, mean K value, suction time, intraocular pressure and central cornea thickness were not significantly different between the two groups. The outlet location of gas diffusing canal (P<0.01, OR 7.16, 95%CI 2.53-20.32) and the corneal astigmatism (P=0.013, OR 0.13, 95%CI 0.03-0.65) were significantly associated with the incidence of OBL by multivariate logistic regression analysis. Visual acuity, efficacy, and safety were comparable between the two groups two months after surgery except for a slightly lower predictability value for the hard OBL eyes. CONCLUSION: The reduction of the incidence of OBL is obvious when the outlet of gas diffusing canal located at the posterior border of the corneoscleral limbus. This is probably consequent to more effectiveness of gas diffusing canal. Corneal astigmatism is also an independent protective factor for OBL formation.