Purpose: The purpose of this study was to compare inflammatory events and graft characteristics 1 month and 6 months after conjunctival limbal autograft (CLAU) with and without intraoperative mitomycin C (MMC). Methods: This study included 69 eyes of 69 patient’s eyes with pterygium. Clinical data concerning patient demography, preoperative examination including pterygium morphology, recurrence clinical assessment, and complications after CLAU with (MMC+) and without (MMC-) intraoperative MMC were all registered at 1 month and 6 months after surgery. Results: Thirty-five eyes were included in MMC+ and 34 in MMC-. Preoperative data were similar in both groups (Student’s t test and Fisher’s exact test; p > 0.05). Thirty-four (49.6%) eyes in the whole sample showed at least one inflammatory complication at 1 month after surgery. MMC- group showed a significantly higher number of cases with complications (p < 0.001; Chi2 test) (MMC+ 28.5%; MMC- 70.5%). No patients presented clinical recurrence at 1 month after surgery. The examination revealed a higher incidence of clinical hyperemia surrounding the surgical site and graft contraction on the host site on the MMC- group, both with statistical signification (p < 0.001; Chi2 test). Although the hemorrhages were less frequent in the MMC- group, there were no significant differences between the two groups (p > 0.05; Chi2 test). Pyogenic granuloma developed at the surgical site in three eyes (4.37%), two of those granulomas were at the MMC- group (p > 0.05). Tendency for recurrences was significantly different between both groups (p = 0.0001; Fisher’s exact test) at the end of 6 months. Thirteen (38%) eyes showed recurrence in MMC- and no cases were displayed in MMC+. Presence of at least 1 inflammatory event was only seen in 16 (23%) cases, all of them in MMC-. Specifically, 15 (44%) eyes showed hyperemia and one (3%) eye presented conjunctival hemorrhages. No new cases of pyogenic granuloma or graft contraction were seen at this time point in both groups. Hyperemia was the only specific event with significant differences between MMC- and MMC+ (p = 0.0001; Fisher’s exact test) at 6 months after surgery. Conclusion: The eyes receiving intraoperative MMC after CLAU seem to present less hyperemia and graft contraction after surgery than those that did not receive MMC as an adjuvant factor. Intraoperative MMC could be associated with a lower recurrence rates.