Purpose To investigate the effect on intraocular pressure (IOP) of intraoperative 5-fluorouracil (5-FU) application during primary trabeculectomy in a West African population. Methods Retrospective case note search of operating theatre records for primary trabeculectomy between 1996 and 2000 in an eye hospital in Lagos, Nigeria. For statistical analysis, patients were divided into group that received intraoperative 5-FU (50 mg/ml for 5 min) and a control group that received no intraoperative antimetabolites. Patients with a follow-up of less than 6 months were excluded. For life-table analysis, only one eye from each patient was included to maintain independent analysis. Results A total of 154 eyes of 101 patients were included in the study. Average follow-up was 17 7 2.18 (95% confidence interval) months. No significant difference was found between the groups for age, sex, preoperative medication, and follow-ups. Comparison of survival curves by the log-rank test showed that the probability of maintaining an IOP of 20 mm Hg or less at 18 months was 76% in the 5-FU group and 79% in the controls (P ¼ 0.55). However, the probability of maintaining an IOP 14 mmHg or less was significantly greater in the 5-FU group (64%) than in the controls (39%, P ¼ 0 .018). Visual acuity loss of more than two Snellen-chart lines was observed in six eyes (7.9%) of the 5-FU group and in four eyes (5.1%) of the control group and this difference was not significant (P ¼ 0.49, Fisher exact test). Complication rates were similar in each group. Conclusions In this population, intraoperative 5-FU application during trabeculectomy appears to improve probability of maintaining an intraocular pressure of 14 mmHg or less with no additional deleterious effects on the eye.