OBJECTIVE To explore the feasibility of intraoperative application of mitomycin C (MMC) in pterygium and observe the ultrastructure change of pterygium with or without intraoperative application of MMC. METHODS Sixty two eyes of 57 patients with primary pterygium were randomly divided into MMC group and control group, 29 patients (32 eyes) in MMC group underwent transposition with intraoperative application of MMC (0.4 mg.ml-1 for 1 minute), whereas 28 patients (30 eyes) in control group underwent transposition. The recurrence rate, complications and side effects were observed and compared between the two groups. The ultrastructure of pterygium with or without intraoperative application of MMC was studied with transmission electron microscopy. The mean follow-up was(7.6 +/- 3.4) months (1-13 minths). RESULTS Eleven eyes of the 30 eyes in control group (36.%) showed recurrence, whereas only 2 of 32 eyes (6.3%) in MMC group showed recurrence (P < 0.005). No severe complication and side effect appeared during the follow-up. Most of fibroblasts in pterygium that underwent intraoperative MMC occurred the change of rough endoplasmic reticulum (RER) dilatation. CONCLUSIONS Intraoperative MMC appears to be an effective treatment in preventing recurrence of primary pterygium. The fibroblasts in pterygium have RER dilatation after application of MMC for 1 minute during the operation.