We measured aqueous flare in 16 glaucomatous eyes after trabeculectomy in which 5-fluorouracil (5-FU) or mitomycin C (MMC) had been used as an adjunctive therapy. The eyes were divided into a 5-FU and an MMC group, matched for factors that might influence the postoperative inflammatory response to intraocular surgery. Seven eyes of seven patients received subconjunctival injections of 5-FU (50 mg in 2 weeks) and nine eyes of nine patients were given 0.2 mg/0.5 mL MMC intraoperatively. The aqueous flare converted to an albumin concentration (mg/dL) was significantly higher in the 5-FU group than in the MMC group (359.6 +/- 113.8 mg/dL and 143.2 +/- 46.7 mg/dL, respectively; Mann-Whitney U test, P < .05) on the second postoperative day. Intraoperative MMC appears to be no more harmful to the blood-aqueous barrier than 5-FU.