OBJECTIVE To determine the minimum effective dosage, most effective route of administration and long-term effects of mitomycin C for prevention of recurrence after pterygium surgery. METHODS In a prospective, masked study, 227 patients undergoing surgery for primary pterygia were assigned randomly to five groups: group 1 received a single intraoperative application of 0.2 mg/ml mitomycin C for 3 minutes; group 2 received a single intraoperative application of 0.4 mg/ml mitomycin C for 3 minutes; group 3 received mitomycin C eye drops 0.2 mg/ml three times daily for 7 days; group 4 received mitomycin C eye drops 0.4 mg/ml three times daily for 14 days; group 5 acted as a control (surgery alone). RESULTS After a mean follow-up time of 28 months, recurrence rates of 6.66%, 4.08%, 4.26%, 4.44%, and 29.27%, respectively, were observed. Statistical analysis showed significant differences between groups receiving mitomycin C and the control (P < or = 0.001). There was no statistical difference among treated groups (P > or = 0.0681). No complications of therapy were observed. CONCLUSIONS These results support the efficacy and relative safety of a single, low-concentration, intraoperative application of mitomycin C in pterygium surgery together with the use of a conjunctival flap, avoiding excessive cauterization of the sclera and leaving bare sclera.