AIM: To study the histological effects of trans-scleral cyclophotocoagulation (TCP) and endoscopic cyclophotocoagulation (ECP) on the ciliary body and other structures collected at autopsy and to compare with untreated controls. Materials and methods: TCP and ECP were performed on human eyes at autopsy. Detailed histological evaluations were perfomed using light microscopy and scanning electron microscopy on treated eyes and compared with untreated controls. RESULTS: Histological changes were observed with both light microscopy and scanning electron microscopy for all treated tissues. Tissue treated with TCP showed pronounced tissue disruption of the ciliary body muscle and stroma, ciliary processes, and both pigmented and non-pigmented ciliary epithelium. ECP-treated tissue exhibited pronounced contraction of the ciliary processes with disruption of the ciliary body epithelium, sparing of the ciliary body muscle and less architectural disorganisation. The sclera was not affected by either laser treatment. CONCLUSIONS: ECP treatment caused less damage to the ciliary body compared with TCP when evaluated by light microscopy and scanning electron microscopy. Compared with TCP, ECP seems to be a more selective form of cyclophotocoagulation, resulting in less tissue disruption while achieving the goal of destroying ciliary body epithelium.