Purpose: To evaluate the morphological changes of the ciliary body after diode laser trans-scleral cyclo-photocoagulation using ultrasound bio-microscopy in refractory glaucoma. Settings: This prospective, interventional, non-comparative, non-randomized, longitudinal study was performed on 40 eyes with refractory glaucoma, during the period between February 2016 and March 2018. Methods: All patients were treated with single session diode laser trans-scleral cyclo-photocoagulation. The intraocular pressure was obtained over a period of 3 months after the operation and morphological changes of the ciliary body were observed using ultrasound bio-microscopy. Results: Trans-scleral cyclo-photocoagulation has achieved a reasonable success in reducing intraocular pressure to less than 22 mm Hg without increasing the number of glaucoma medication. The overall success rate was 40%, as the intraocular pressure decreased from a baseline mean value of 54.70 ± 12.27 to 42.45 ± 9.85 mm Hg 1 week after operation, 33.50 ± 8.00 mm Hg after 1 month, and 25.60 ± 6.62 after 3 months of operation. Ultrasound bio-microscopy detected reduction in the length and width of ciliary processes in addition to the ciliary muscle thickness of the treated quadrants. Intraocular pressure was more correlated to the width of the ciliary processes. Conclusion: Trans-scleral cyclo-photocoagulation is a rapid and effective procedure in treatment of refractory glaucoma with intraocular pressure reduction. Ultrasound bio-microscopy is a promising twin tool for cyclo-destructive procedures to detect ciliary body changes and can be used as a guide for re-treatment procedures.