To compare the recurrence of pterygium between free conjunctival auto-graft and conjunctival rotation flap following simple surgical excision of pterygium.Quasi-experimental study.Shifa Foundation Community Health Clinic, Shifa College of Medicine, Islamabad, from January to November 2012.Fifty seven cases aged above 18 years, with a pterygium corneal encroachment of ³ 2 mm which was responsible for visual disability or was cosmetically undesirable were recruited for the study and randomly assigned to conjunctival auto-graft group and conjunctival rotation flap group. Cases with a history of glaucoma or glaucoma suspect, prior pterygium surgery, pterygium with concurrent ocular surface and lid disease, conjunctival inflammation and scarring, pseudo-pterygium or collagen vascular disease were excluded. After simple pterygium excision conjunctival auto-graft group (n=26) cases received a free conjunctival flap was transplanted, while conjunctival rotation flap group (n=31) cases received a conjunctival rotation flap. All cases were followed-up for 6 months after surgery for recurrence and complications. Frequency distribution and significance of association of recurrence using Fisher's exact test and Mann-Whitney U-test was carried out using Statistical Package for Social Sciences (SPSS) version 20.The median (and inter-quartile range) age and surgery duration in conjunctival auto-graft group and conjunctival rotation flap group were 60 (51.50-63.00) and 57 (45.00-60.00) years, 28.50 (27.00-30.50) and 16.00 (15.00-17.00) minutes respectively. Recurrence was seen in 2 (7.96%) and 3 (9.76%) cases in auto-graft and rotation flap groups respectively. No significant difference was seen in postoperative complications between the two groups (p=0.60).The surgical time for conjunctival rotation flap procedure is less as compared to free auto-graft, while their recurrence and complications are comparable.