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Abstract Background To propose that possible alteration or damage to the ciliary zonules during uncomplicated endoscopic cyclophotocoagulation (ECP) can cause complications in subsequent filtration surgery. Case presentation We present two cases with uncomplicated primary combined phacoemulsification and ECP that underwent subsequent trabeculectomy. Both cases were complicated with vitreous prolapse during the trabeculectomy procedure. We review the anatomy of the ciliary zonules and their spatial relationship with the ciliary processes targeted during ECP and propose an association between ECP, zonular damage and complications in subsequent trabeculectomy such as vitreous prolapse. Conclusions Damage to ciliary zonules during ECP may not manifest until subsequent glaucoma filtration surgery. In patients who received prior ECP, we may consider taking preventative measures to avoid associated complications such as vitreous prolapse. Patients with known risk factors for weak zonules may consider choosing alternative intraocular pressure-lowering means.