Purpose To evaluate the intraocular pressure (IOP)-lowering effect and ocular side effects of daunorubicin (DNR) in drug-modulated trabeculectomy. Methods A prospective pilot study was conducted in which 21 Asian patients of Indian origin with high risk factors for failure of trabeculectomy were recruited. An approval from research ethics committee and an informed consent from every patient included in the study were obtained. DNR, an antimetabolite with known antifibroblastic action was used intraoperatively. A limbusbased conjunctival flap followed by conventional trabeculectomy was performed in all eyes. During trabeculectomy, a cellulose sponge soaked in 0.2 mg/ml DNR was applied for 3 min at the proposed site of trabeculectomy before preparation of the partial thickness scleral flap. A regular followup was carried out for 1 year where parameters including visual acuity, IOP by applanation tonometry, and slit lamp examination were performed on each visit. An IOP of 21 mmHg or less was taken as criteria for success. Results Following DNR trabeculectomy, the IOP was lowered from baseline preoperative value of 36.1975.9 to 16.0572.52 mmHg at the end of 1 year. Success rate of 81% (17 out of 21 patients) was noted. None of the patients developed corneal epithelial toxicity, hypotony maculopathy, or choroidal detachment. Conclusion The authors feel that intraoperative daunorubicin is safe and effective in lowering IOP in high-risk surgical cases of glaucoma. However, a much larger cohort study over a considerable number of years will eventually demonstrate its safety.