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Glaucoma, the consequence of Axenfeld–Rieger syndrome (ARS) can develop in 50% of patients. It can cause complete permanent blindness if not given appropriate management. A twenty-one-year-old woman came to the clinic with blurred vision in both eyes since the last 3 years, pain in both eyes and headache since the last 2 years and previously medicated. Visual acuity (VA) was 1/60 in both eyes and intraocular pressures (IOP) were 46 mmHg and 37 mmHg respectively. The right eye (RE) showed prominent Schwalbe's line, posterior embryotoxon, corectopia, pseudopolycoria, and diffuse iris stromal hypoplasia. The left eye (LE) showed iris hypoplasia. Gonioscopy revealed iris adhesions in both eyes. Size of cup to disc ratio (CDR) was 0.7 with peripapillary atrophy and myopic crescent in the LE. Humphrey Visual Field (HVF) showed an arcuate defect superiorly, multiple defects in inferior quadrant of the RE and superior arcuate, nasal step in the LE. Non-ocular abnormalities consisted of configuration craniofacial dysmorphism hypertelorism, telecanthus, mid-facial hypoplasia, paraumbilical skin tags, microdontia, hypoplasia, and partial anodontia. We planned trabeculectomy with 5-fluorouracil for both eyes (BE). It has been done in LE. LE uncorrected visual acuity becomes 5/60 and the IOP reduce to 9 mmHg in the 14th day of surgery. Glaucoma in Axenfeld–Rieger syndrome could be treated by trabeculectomy with 5FU.