Ninety-five patients (104 eyes) were enrolled in a pilot study of subconjunctival 5-fluorouracil (5-FU) injections after filtering surgery in eyes with poor surgical prognoses. At least a six-month follow-up was available on 84 patients, of whom four were excluded from the analysis of surgical outcome because they suffered retinal detachments within six months of their filtering surgery. The initial 5-FU procedures on the remaining 80 patients were successful (no further glaucoma surgical procedures were either performed or recommended, and the intraocular pressures [IOPs] were either 21 mmHg or lower with ocular hypotensive medication[s] or 25 mmHg or lower without ocular hypotensive medication) in 33 (68%) of the 48 aphakic eyes with non-neovascular glaucomas, 13 (81%) of the 16 phakic eyes with non-neovascular glaucomas after unsuccessful filtering surgery, and 12 (75%) of the 16 eyes with neovascular glaucoma (NVG). The follow-up on the successful eyes ranged from 6 to 34 months (mean +/- SD = 18.5 +/- 7.5). The visual acuities remained within one line of their preoperative levels or improved in 38 (79%) of the 48 aphakic eyes with non-neovascular glaucoma, 11 (69%) of the 16 phakic eyes with non-neovascular glaucoma after unsuccessful filtering surgery, and 12 (75%) of the 16 eyes with NVG. The initial 5-FU procedures on the 104 eyes were complicated by the following: corneal epithelial defects (50%); conjunctival wound and suture tract leaks (36%; 2% underwent surgical repair); suprachoroidal hemorrhages (9%); retinal detachments (3%); subepithelial corneal scarring (3%); endophthalmitis (2%); and malignant glaucoma (1%). It is the authors' impression that postoperative subconjunctival 5-FU increases the likelihood of achieving IOP control after filtering surgery in eyes with poor surgical prognoses; however, a randomized clinical trial is necessary to confirm this impression.